{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/comments/30944430","id":30944430,"diff_hunk":"@@ -184,139 +346,534 @@\n         <param name=\"peak_lists\" format=\"mgf\" type=\"data\" multiple=\"true\" label=\"Input Peak Lists (mgf)\"\n             help=\"Select appropriate MGF dataset(s) from history\" />\n \n-        <expand macro=\"general_options\"/>\n-\n-        <param name=\"correct_titles\" type=\"select\" label=\"How should PeptideShaker deal with duplicate spectra?\"\n-            help=\"Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option\">\n-            <option value=\"0\">no correction</option>\n-            <option value=\"1\" selected=\"True\">rename spectra</option>\n-            <option value=\"2\">delete spectra</option>\n+\t    <!-- Search Engine Selection -->\n+        <param name=\"engines\" type=\"select\" display=\"checkboxes\" multiple=\"True\" label=\"DB-Search Engines\">\n+            <option value=\"X!Tandem\" selected=\"True\">X!Tandem</option>\n+            <option value=\"MyriMatch\">MyriMatch</option>\n+            <!--<option value=\"MS_Amanda\">MS_Amanda</option> -->\n+            <option value=\"MSGF\" selected=\"True\">MS-GF+</option>\n+            <option value=\"OMSSA\" selected=\"True\">OMSSA</option>\n+            <option value=\"Comet\">Comet</option>\n+            <option value=\"Tide\">Tide</option>\n+            <validator type=\"no_options\" message=\"Please select at least one output file\" />\n         </param>\n \n-        <param name=\"missing_titles\" type=\"boolean\" checked=\"false\" truevalue=\"-missing_titles 1\" falsevalue=\"-missing_titles 0\"\n-            label=\"Add missing spectrum titles\" help=\"(-missing_titles)\"/>\n \n-        <param name=\"mgf_splitting\" type=\"integer\" value=\"1000\" label=\"The maximum mgf file size in MB before splitting the mgf\"\n-            help=\"Choose a smaller value if you are running on a machine with limited memory\"/>\n \n-        <param name=\"mgf_spectrum_count\" type=\"integer\" value=\"25000\" label=\"The maximum number of spectra per mgf file when splitting\"\n-            help=\"Choose a smaller value if you are running on a machine with limited memory\"/>\n+\t\t<!-- General Parameters -->\n+        <expand macro=\"general_options\"/>\n \n-        <conditional name=\"advanced\">\n-            <param name=\"advanced_type_selector\" type=\"select\" label=\"Basic or Advanced Search options\">\n-                <option value=\"basic\" selected=\"True\">Basic</option>\n+\t\t<!-- Optional Advanced SearchGUI Parameters -->\n+        <conditional name=\"searchgui_advanced\">\n+            <param name=\"searchgui_advanced_selector\" type=\"select\" label=\"SearchGUI Options\">\n+                <option value=\"basic\" selected=\"True\">Default</option>\n                 <option value=\"advanced\">Advanced</option>\n             </param>\n             <when value=\"basic\" />\n             <when value=\"advanced\">\n-                <conditional name=\"xtandem\">\n-                    <param name=\"xtandem_selector\" type=\"select\" label=\"Run X!Tandem search\">\n-                        <option value=\"yes\" selected=\"True\">Search with X!Tandem</option>\n-                        <option value=\"no\">No X!Tandem search</option>\n-                    </param>\n-                    <when value=\"no\" />\n-                    <when value=\"yes\">\n-                        <param name=\"xtandem_npeaks\" type=\"integer\" value=\"50\" \n-                            label=\"X!Tandem: Total Peaks\" help=\"Maximum number of peaks to be used from a spectrum\"/>\n-                        <param name=\"xtandem_min_peaks\" type=\"integer\" value=\"15\" \n-                            label=\"X!Tandem: Min Peaks\" help=\"Minimum number of peaks required for a spectrum to be considered\"/>\n-                        <param name=\"xtandem_min_frag_mz\" type=\"integer\" value=\"200\" \n-                            label=\"X!Tandem: Min Frag m/z\" help=\"Fragment mass peaks with m/z less than this value will be discarded\"/>\n-                        <param name=\"xtandem_min_prec_mass\" type=\"integer\" value=\"200\" \n-                            label=\"X!Tandem: Min Precursor Mass\" help=\"Minimum mass of 1+ mass of parent ion to be considered\"/>\n-                        <param name=\"xtandem_noise_suppr\" type=\"boolean\" checked=\"true\" truevalue=\"1\" falsevalue=\"0\"\n-                            label=\"X!Tandem: Noise Suppression\" help=\"Use noise suppression\"/>\n-\n-                        <conditional name=\"xtandem_refine\"><!-- -xtandem_refine -->\n-                            <param name=\"xtandem_refine_selector\" type=\"select\" label=\"X!Tandem peptide model refinement\">\n-                                <option value=\"no\" selected=\"True\">Don't refine</option>\n-                                <option value=\"yes\" >Use refinement</option>\n-                            </param>\n-                            <when value=\"no\"/>\n-                            <when value=\"yes\">\n-                                <param name=\"xtandem_refine_unc\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\"\n-                                    label=\"X!Tandem: Unanticipated cleavage, refinement\" help=\"Allow for unanticipated cleavage during refinement\"/>\n-                                <param name=\"xtandem_refine_semi\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" \n-                                    label=\"X!Tandem: Cleavage semi, refinement\" help=\"Search for semi-tryptic peptides during refinement\"/>\n-                                <param name=\"xtandem_refine_p_mut\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" \n-                                    label=\"X!Tandem: Point mutations, refinement\" help=\"Allow for point mutations during refinement\"/>\n-                                <param name=\"xtandem_refine_snaps\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" \n-                                    label=\"X!Tandem: snAPs, refinement\" help=\"Search for known single amino acid polymorphisms during refinement\"/>\n-                                <param name=\"xtandem_refine_spec_synt\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" \n-                                    label=\"X!Tandem: Spectrum synthesis, refinement\" help=\"Use spectrum synthesis scoring\"/>\n-                            </when>\n-                        </conditional>\n-                    </when>\n-                </conditional>\n+\t\t    <param name=\"correct_titles\" type=\"select\" label=\"How should PeptideShaker deal with duplicate spectra?\"\n+\t\t        help=\"Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option\">\n+\t\t        <option value=\"0\">no correction</option>\n+\t\t        <option value=\"1\" selected=\"True\">rename spectra</option>\n+\t\t        <option value=\"2\">delete spectra</option>\n+\t\t    </param>\n+\n+\t\t    <param name=\"missing_titles\" type=\"boolean\" checked=\"false\" truevalue=\"-missing_titles 1\" falsevalue=\"-missing_titles 0\"\n+\t\t        label=\"Add missing spectrum titles\" help=\"(-missing_titles)\"/>\n+\n+\t\t    <param name=\"mgf_splitting\" type=\"integer\" value=\"1000\" label=\"The maximum mgf file size in MB before splitting the mgf\"\n+\t\t        help=\"Choose a smaller value if you are running on a machine with limited memory\"/>\n+\n+\t\t    <param name=\"mgf_spectrum_count\" type=\"integer\" value=\"25000\" label=\"The maximum number of spectra per mgf file when splitting\"\n+\t\t        help=\"Choose a smaller value if you are running on a machine with limited memory\"/>\n+        </when>\n+        </conditional>\n \n-                <conditional name=\"omssa\">\n-                    <param name=\"omssa_selector\" type=\"select\" label=\"Run OMSSA search\">\n-                        <option value=\"yes\" selected=\"True\">Search with OMSSA</option>\n-                        <option value=\"no\">No OMSSA search</option>\n+     \n+    \t<!-- X!TANDEM ADVANCED PARAMETERS -->\n+        <conditional name=\"xtandem\">\n+            <param name=\"xtandem_advanced\" type=\"select\" label=\"X!Tandem Options\">\n+                <option value=\"yes\">Advanced</option>\n+                <option value=\"no\" selected=\"True\">Default</option>\n+            </param>\n+            <when value=\"no\" />\n+            <when value=\"yes\">\n+            \t<param name=\"xtandem_npeaks\" type=\"integer\" value=\"50\" \n+                    label=\"X!Tandem: Total Peaks\" help=\"Maximum number of peaks to be used from a spectrum\"/>\n+                <param name=\"xtandem_min_peaks\" type=\"integer\" value=\"15\" \n+                    label=\"X!Tandem: Min Peaks\" help=\"Minimum number of peaks required for a spectrum to be considered\"/>\n+                <param name=\"xtandem_min_frag_mz\" type=\"integer\" value=\"200\" \n+                    label=\"X!Tandem: Min Frag m/z\" help=\"Fragment mass peaks with m/z less than this value will be discarded\"/>\n+                <param name=\"xtandem_min_prec_mass\" type=\"integer\" value=\"200\" \n+                    label=\"X!Tandem: Min Precursor Mass\" help=\"Minimum mass of 1+ mass of parent ion to be considered\"/>\n+                <param name=\"xtandem_noise_suppr\" type=\"boolean\" checked=\"true\" truevalue=\"1\" falsevalue=\"0\"\n+                    label=\"X!Tandem: Noise Suppression\" help=\"Use noise suppression\"/>\n+\t\t\t\t<param name=\"xtandem_dynamic_range\" help=\"Sets the dynamic range for scoring spectra\"\n+\t\t\t\t\tlabel=\"X!Tandem: Dynamic Range\" value=\"100\" type=\"integer\" />\n+\t\t\t\t<param name=\"xtandem_quick_acetyl\" help=\"Protein N-terminal modification detection\"\n+\t\t\t\t\tlabel=\"X!Tandem: Quick Acetyl\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" />\n+\t\t\t\t<param name=\"xtandem_quick_pyro\" help=\"Peptide N-terminus cyclization detection\"\n+\t\t\t\t\tlabel=\"X!Tandem: Quick Pyrolidone\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" /> \n+\t\t\t\t<param name=\"xtandem_stp_bias\" help=\"Interpretation of peptide phosphorylation models\"\n+\t\t\t\t\tlabel=\"X!Tandem: Protein stP Bias\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\" /> \n+\t\t\t\t<param name=\"xtandem_evalue\" help=\"Highest value for recorded peptides\"\n+\t\t\t\t\tlabel=\"X!Tandem: Maximum Valid Expectation Value\" type=\"float\" value=\"100\" />\n+\t\t\t\t<param name=\"xtandem_output_proteins\" help=\"Controls output of protein sequences\"\n+\t\t\t\t\tlabel=\"X!Tandem: Output Proteins\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\" />\n+\t\t\t\t<param name=\"xtandem_output_sequences\" help=\"Controls output of sequence information\"\n+\t\t\t\t\tlabel=\"X!Tandem: Output Sequences\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\" />\n+\t\t\t\t<param name=\"xtandem_output_spectra\" help=\"Controls output of spectrum information\"\n+\t\t\t\t\tlabel=\"X!Tandem: Output Spectra\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\" />\n+\t\t\t\t<!-- <param name=\"xtandem_skyline_path\" label=\"X!Tandem 'spectrum, skyline path'\" type=\"text\" help=\"Path to a spectrum data file for use by skyline.\" -->\n+\t\t\t\t\t\n+                <conditional name=\"xtandem_refine\"><!-- -xtandem_refine -->\n+                    <param name=\"xtandem_refine_selector\" type=\"select\" label=\"X!Tandem peptide model refinement\">\n+                        <option value=\"no\" selected=\"True\">Don't refine</option>\n+                        <option value=\"yes\" >Use refinement</option>\n                     </param>\n-                    <when value=\"no\" />\n+                    <when value=\"no\"/>\n                     <when value=\"yes\">\n-                        <param name=\"hitlist_length\" label=\"OMSSA: Hit List Length\" type=\"integer\" value=\"25\" />\n-                        <param name=\"remove_precursor\" label=\"OMSSA: Remove Precurosr\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"/>\n-                        <param name=\"scale_precursor\" label=\"OMSSA: Scale Precursor Mass\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"/>\n-                        <param name=\"estimate_charge\" label=\"OMSSA: Estimate Charge\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" />\n+                        <param name=\"xtandem_refine_unc\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"\n+                            label=\"X!Tandem: Unanticipated cleavage, refinement\" help=\"Allow for unanticipated cleavage during refinement\"/>\n+                        <param name=\"xtandem_refine_semi\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"\n+                            label=\"X!Tandem: Cleavage semi, refinement\" help=\"Search for semi-tryptic peptides during refinement\"/>\n+                        <param name=\"xtandem_refine_p_mut\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"\n+                            label=\"X!Tandem: Point mutations, refinement\" help=\"Allow for point mutations during refinement\"/>\n+                        <param name=\"xtandem_refine_snaps\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"\n+                            label=\"X!Tandem: snAPs, refinement\" help=\"Search for known single amino acid polymorphisms during refinement\"/>\n+                        <param name=\"xtandem_refine_spec_synt\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"\n+                            label=\"X!Tandem: Spectrum synthesis, refinement\" help=\"Use spectrum synthesis scoring\"/>\n+                        <param name=\"xtandem_refine_pot\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"\n+                            label=\"X!Tandem: Use potential modifications, refinement\" help=\"Controls the use of refinement modifications in all refinement modules.\"/>\n+                        <param name=\"xtandem_refine_evalue\" help=\"Highest value for recorded peptides during refinement\"\n+\t\t\t\t\t\t\tlabel=\"X!Tandem: Maximum Valid Expectation Value, refinement\" type=\"float\" value=\"0.01\" />\n                     </when>\n                 </conditional>\n+            </when>\n+        </conditional>\n+\t\t\t\t\t\t\n+\t\t<!-- OMSSA ADVANCED PARAMETERS -->\n+        <conditional name=\"omssa\">\n+            <param name=\"omssa_advanced\" type=\"select\" label=\"OMSSA Options\">\n+                <option value=\"yes\">Advanced</option>\n+                <option value=\"no\" selected=\"True\">Default</option>\n+            </param>\n+            <when value=\"no\" />\n+            <when value=\"yes\">\n+                <param name=\"hitlist_length\" label=\"OMSSA: Hit List Length\" type=\"integer\" value=\"25\" />\n+                <param name=\"remove_precursor\" label=\"OMSSA: Remove Precurosr\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"/>\n+                <param name=\"scale_precursor\" label=\"OMSSA: Scale Precursor Mass\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"/>\n+                <param name=\"estimate_charge\" label=\"OMSSA: Estimate Charge\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" />\n+                \n+                <param name=\"omssa_memory\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"\n+                \tlabel=\"OMSSA: Map Sequences in Memory\" help=\"Use memory mapped sequence libraries\" />\n+    \t  \t\t<!-- param name=\"omssa_isotopes\" type=\"integer\" value=\"0\" \n+    \t  \t\t\tlabel=\"OMSSA: Number of Isotopes\" help=\"Number of isotopes to use (integer), 0 implies monoisotopic (default)\" / -->\n+   \t    \t\t<param name=\"omssa_neutron\" type=\"float\" value=\"1446.94\" \n+   \t    \t\t\tlabel=\"OMSSA: Neutron Mass\" help=\"Mass after which OMSSA should consider neutron exact mass\" />\n+    \t    \t<param name=\"omssa_low_intensity\" type=\"float\" value=\"0.0\" \n+    \t    \t\tlabel=\"OMSSA: Low Intensity Cutoff\" help=\"Low intensity cutoff as a fraction of max peak\" />\n+    \t    \t<param name=\"omssa_high_intensity\" type=\"float\" value=\"0.2\" \n+    \t    \t\tlabel=\"OMSSA: High Intensity Cutoff\" help=\"High intensity cutoff as a fraction of max peak\" />\n+   \t    \t\t<param name=\"omssa_intensity_incr\" type=\"float\" value=\"0.0005\" \n+   \t    \t\t\tlabel=\"OMSSA: Intensity Increment\" help=\"Intensity increment\" />\n+    \t    \t<param name=\"omssa_single_window_wd\" type=\"integer\" value=\"27\" \n+    \t    \t\tlabel=\"OMSSA: Single Charge Window Width\" help=\"Single charge window width in Da (integer)\" />\n+    \t    \t<param name=\"omssa_double_window_wd\" type=\"integer\" value=\"14\" \n+    \t    \t\tlabel=\"OMSSA: Double Charge Window Width\" help=\"OMSSA double charge window width in Da (integer)\" />\n+    \t    \t<param name=\"omssa_single_window_pk\" type=\"integer\" value=\"2\" \n+    \t    \t\tlabel=\"OMSSA: Single Charge Window Peaks\" help=\"Minimum number of peaks in single charge window (integer)\" />\n+    \t    \t<param name=\"omssa_double_window_pk\" type=\"integer\" value=\"2\" \n+    \t    \t\tlabel=\"OMSSA: Double Charge Window Peaks\" help=\"Minimum number of peaks in double charge window (integer)\" />\n+    \t    \t<param name=\"omssa_min_ann_int_pks\" type=\"integer\" value=\"6\" \n+    \t    \t\tlabel=\"OMSSA: Minimum Number of Annotated Peaks of Intense Ones\" help=\"Minimum number of annotated peaks among the most intense ones\" />\n+        \t\t<param name=\"omssa_min_annotated_peaks\" type=\"integer\" value=\"2\" \n+        \t\t\tlabel=\"OMSSA: Minimum number of Annotated Peaks\" help=\"Minimum number of annotated peaks\" />\n+   \t    \t\t<param name=\"omssa_min_peaks\" type=\"integer\" value=\"4\" \n+   \t    \t\t\tlabel=\"OMSSA: Minimum Peak Count\" help=\"The minimum number of m/z values a spectrum must have to be searched\" />\n+    \t    \t<param name=\"omssa_methionine\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"\n+    \t    \t\tlabel=\"OMSSA: Cleave n-term Methionine\" help=\"Allow for N-terminal methionine cleavage\" />\n+    \t    \t<param name=\"omssa_max_ladders\" type=\"integer\" value=\"128\" \n+    \t    \t\tlabel=\"OMSSA: Maximum Number of m/z Ladders\" help=\"The maximum number of mass ladders to generate per database peptide\" />\n+    \t    \t<param name=\"omssa_max_frag_charge\" type=\"integer\" value=\"2\" \n+    \t    \t\tlabel=\"OMSSA: Maximum Fragment Charge\" help=\"Maximum fragment charge\" />\n+    \t    \t<param name=\"omssa_fraction\" type=\"float\" value=\"0.95\" \n+    \t    \t\tlabel=\"OMSSA: Fraction of Peaks to estimate Charge 1\" help=\"fraction of peaks to estimate charge 1\" />\n+    \t    \t<param name=\"omssa_plus_one\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" \n+    \t    \t\tlabel=\"OMSSA: Estimate Plus One Charge\" help=\"Allow OMSSA to estimate plus one charge algorithmically\"/>\n+    \t    \t<param name=\"omssa_charge\" type=\"select\" \n+    \t    \t\tlabel=\"OMSSA: Fragment Charge\" help=\"OMSSA fragment charge option\" >\n+                <option value=\"0\" >Minus</option>\n+                <option value=\"1\" selected=\"True\">Plus</option>\n+    \t    \t</param>\n+    \t    \t<param name=\"omssa_prec_per_spectrum\" type=\"integer\" value=\"1\" \n+    \t    \t\tlabel=\"OMSSA: Minimum Number of Precursors per Spectrum\" help=\"Minimum number of precursors per spectrum\" />\n+    \t    \t<param name=\"omssa_forward\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" \n+    \t    \t\tlabel=\"OMSSA: Include First Forward Ion (b1) in Search\" help=\"Allow OMSSA to include first forward ion (b1) in search\" />\n+    \t    \t<param name=\"omssa_rewind\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"  \n+    \t    \t\tlabel=\"OMSSA: Search Rewind\" help=\"Allow search rewind (C-terminal) ions\" />\n+\t\t\t\t<param name=\"omssa_max_frag_series\" type=\"integer\" value=\"100\" \n+    \t    \t\tlabel=\"OMSSA: Maximum Fragment per Series\" help=\"Max number of fragments ions ions in each series being searched\" />\n+    \t    \t<param name=\"omssa_corr\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" \n+    \t    \t\tlabel=\"OMSSA: Use Correlation Correction\" help=\"Allow the use correlation correction score\" />\n+    \t    \t<param name=\"omssa_consecutive_p\" type=\"float\" value=\"0.5\" \n+    \t    \t\tlabel=\"OMSSA: Consecutive Ion Probability\" help=\"Probability of consecutive ion (used in correlation correction)\" />\n+    \t    \t<param name=\"omssa_it_sequence_evalue\" type=\"float\" value=\"0.0\" \n+    \t    \t\tlabel=\"OMSSA: Sequence e-value Cutoff\" help=\"The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)\" />\n+    \t    \t<param name=\"omssa_it_spectrum_evalue\" type=\"float\" value=\"0.01\" \n+    \t    \t\tlabel=\"OMSSA: Spectrum e-value Cutoff\" help=\"The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)\" />\n+    \t    \t<param name=\"omssa_it_replace_evalue\" type=\"float\" value=\"0.01\" \n+    \t    \t\tlabel=\"OMSSA: Replace e-value cutoff\" help=\"The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)\" />\n+    \t    \t<param name=\"omssa_remove_prec\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\" \n+    \t    \t\tlabel=\"OMSSA: Remove Precursor\" help=\"Remove precursors\" />\n+\t\t\t\t<param name=\"omssa_scale_prec\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"  \n+    \t    \t\tlabel=\"OMSSA: Scale Precursor Mass\" help=\"scale precursor mass\" />\n+    \t    \t<param name=\"omssa_estimate_charge\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"  \n+    \t    \t\tlabel=\"OMSSA: Remove Precursor\" help=\"Remove precursors\" />\n+    \t    \t<param name=\"omssa_max_evalue\" type=\"float\" value=\"100\" \n+    \t    \t\tlabel=\"OMSSA: Maximal evalue Considered\" help=\"The maximum e-value considered\" />\n+    \t    \t<param name=\"omssa_remove_prec\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"  \n+    \t    \t\tlabel=\"OMSSA: Estimate Precursor Charge\" help=\"Allow estimation of precursor charge\" />\n+    \t    \t<param name=\"omssa_it_replace_evalue\" type=\"float\" value=\"100\" \n+    \t    \t\tlabel=\"OMSSA: Maximal evalue\" help=\"The maximum OMSSA e-value considered\" />\n+    \t    \t<param name=\"omssa_hitlist_length\" type=\"integer\" value=\"0\" \n+    \t    \t\tlabel=\"OMSSA: Hitlist Length\" help=\"OMSSA hitlist length, 0 means all\" />\n+        \t\t<param name=\"omssa_hitlist_charge\" type=\"integer\" value=\"30\" \n+        \t\t\tlabel=\"OMSSA: Number of Hits per Spectrum per Charge\" help=\"number of hits per spectrum per charge\" />\n+\t   \t\t \t<param name=\"omssa_min_pep_length\" type=\"integer\" value=\"4\" \n+\t   \t\t \t\tlabel=\"OMSSA: Minumum Peptide Length\" help=\"Minimum length of peptides for no-enzyme and semi-tryptic searches\" />\n+\t   \t \t\t<param name=\"omssa_max_pep_length\" type=\"integer\" value=\"40\" \n+\t   \t \t\t\tlabel=\"OMSSA: Maximum Peptide Length\" help=\"Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)\" />\n+\t   \t \t\t<param name=\"omssa_format\" label=\"OMSSA output format\" type=\"select\" >\n+                \t<option value=\"0\" selected=\"True\">OMX</option>\n+                \t<option value=\"1\" >CSV</option>\n+                </param> \n+\t\t\t\t\n+            </when>\n+        </conditional>\n \n-                <conditional name=\"msgf\">\n-                    <param name=\"msgf_selector\" type=\"select\" label=\"Run MSGF search\">\n-                        <option value=\"yes\" selected=\"True\">Search with MSGF</option>\n-                        <option value=\"no\">No MSGF search</option>\n-                    </param>\n-                    <when value=\"no\" />\n-                    <when value=\"yes\">\n-                        <param name=\"msgf_decoy\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\"\n-                            label=\"Search Decoys\" help=\"If yes then a decoy database will be generated and searched. Assumed input database contains no decoys\"/>\n-                        <param name=\"msgf_min_pep_length\" type=\"integer\" value=\"6\"\n-                            label=\"Minimum Peptide Length\" help=\"Minimum length for a peptide to be considered\"/>\n-                        <param name=\"msgf_max_pep_length\" type=\"integer\" value=\"30\" \n-                            label=\"Maximum Peptide Length\" help=\"Maximum length for a peptide to be considered\"/>\n-                        <param name=\"msgf_termini\" type=\"select\" format=\"text\" \n-                            label=\"Number of tolerable termini\" help=\"Searches will take much longer if selecting a value other than 2\">\n-                            <option value=\"0\">0 (ie non-specific cleavage)</option>\n-                            <option value=\"1\">1 (ie semi-tryptic cleavage)</option>\n-                            <option value=\"2\" selected=\"true\">2 (ie fully-tryptic cleavage)</option>\n-                        </param>\n-                        <param name=\"msgf_num_ptms\" label=\"Max PTMs per peptide\" type=\"integer\" value=\"2\"/>\n-                    </when>\n-                </conditional>\n+\t\t<!-- MS-GF+ ADVANCED PARAMETERS -->\n+        <conditional name=\"msgf\">\n+            <param name=\"msgf_advanced\" type=\"select\" label=\"MSGF Options\">\n+                <option value=\"yes\">Advanced</option>\n+                <option value=\"no\" selected=\"True\">Default</option>\n+            </param>\n+            <when value=\"no\" />\n+            <when value=\"yes\">\n+                <param name=\"msgf_decoy\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\"\n+                    label=\"MSGF: Search Decoys\" help=\"If yes then a decoy database will be generated and searched. Assumed input database contains no decoys\"/>\n+                <param name=\"msgf_min_pep_length\" type=\"integer\" value=\"6\"\n+                    label=\"MSGF: Minimum Peptide Length\" help=\"Minimum length for a peptide to be considered\"/>\n+                <param name=\"msgf_max_pep_length\" type=\"integer\" value=\"30\" \n+                    label=\"MSGF: Maximum Peptide Length\" help=\"Maximum length for a peptide to be considered\"/>\n+                <param name=\"msgf_termini\" type=\"select\" format=\"text\" \n+                    label=\"MSGF: Number of tolerable termini\" help=\"Searches will take much longer if selecting a value other than 2\">\n+                    <option value=\"0\">0 (ie non-specific cleavage)</option>\n+                    <option value=\"1\">1 (ie semi-tryptic cleavage)</option>\n+                    <option value=\"2\" selected=\"true\">2 (ie fully-tryptic cleavage)</option>\n+                </param>\n+                <param name=\"msgf_num_ptms\" label=\"MSGF: Max PTMs per peptide\" type=\"integer\" value=\"2\"/>\n+                \n+\t\t\t    <param name=\"msgf_instrument\" label=\"MSGF: Instrument type\" type=\"select\" help=\"Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)\">\n+\t\t\t                \t<option value=\"0\" selected=\"True\">Low-res LCQ/LTQ</option>\n+\t\t\t                \t<option value=\"1\" >High-res LTQ</option>\n+\t\t\t                \t<option value=\"2\" >TOF</option>\n+\t\t\t                \t<option value=\"3\" >Q-Exactive</option>\n+\t\t\t    </param>\n+\t\t\t    <param name=\"msgf_fragmentation\" label=\"MSGF: Fragmentation type\" type=\"select\" help=\"Fragmentation method identifier (used to determine the scoring model)\">\n+\t\t\t                \t<option value=\"0\" selected=\"True\">As written in the spectrum or CID if no info</option>\n+\t\t\t                \t<option value=\"1\" >CID</option>\n+\t\t\t                \t<option value=\"2\" >ETD</option>\n+\t\t\t                \t<option value=\"3\" >HCD</option>\n+\t\t\t    </param>\n+\t\t\t    <param name=\"msgf_protocol\" label=\"MSGF: Protocol type\" type=\"select\" help=\"Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples\">\n+\t\t\t                \t<option value=\"0\" selected=\"True\">Automatic</option>\n+\t\t\t                \t<option value=\"1\" >Phosphorylation</option>\n+\t\t\t                \t<option value=\"2\" >iTRAQ</option>\n+\t\t\t                \t<option value=\"3\" >iTRAQPhospho</option>\n+\t\t\t                \t<option value=\"4\" >TMT</option>\n+\t\t\t                \t<option value=\"5\" >Standard</option>\n+\t\t\t    </param>\n+\t\t\t    <param name=\"msgf_num_matches\" label=\"MSGF: Maximum Number of Spectrum Matches\" type=\"integer\" value=\"1\" help=\"Number of peptide matches per spectrum to report\" />\n+\t\t\t    <param name=\"msgf_additional\" label=\"MS-GF+ additional features\" type=\"select\" help=\"Additional features to export\">\n+\t\t\t             \t\t<option value=\"0\" selected=\"True\">output basic scores only</option>\n+\t\t\t                \t<option value=\"1\" >output additional features</option>\n+\t\t\t    </param>\n+\t\t\t    <param name=\"msgf_isotope_low\" label=\"MSGF: Lower Isotope Error Range\" type=\"integer\" value=\"0\" help=\"Lower isotope error range\" />\n+\t\t\t    <param name=\"msgf_isotope_high\" label=\"MSGF: Upper Isotope Error Range\" type=\"integer\" value=\"1\" help=\"Upper isotope errror range\" /> \n+            </when>\n+        </conditional>\n+\n+<!--  \t\tMS-AMANDA ADVANCED PARAMETERS \n+        <conditional name=\"ms_amanda\">\n+            <param name=\"ms_amanda_advanced\" type=\"select\" label=\"MS Amanda Options\">\n+                <option value=\"yes\" selected=\"True\">Advanced</option>\n+                <option value=\"no\">Default</option>\n+            </param>\n+            <when value=\"no\" />\n+            <when value=\"yes\">\n+            \t<param name=\"ms_amanda_decoy\"  type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"false\" \n+            \t\tlabel=\"MS Amanda: Generate Decoys\" help=\"generate decoys\" />\n+\t\t\t\t<param name=\"ms_amanda_max_evalue\" type=\"float\" value=\"100\" \n+\t\t\t\t\tlabel=\"MS Amanda: Maximal Evalue\" help=\"MS Amanda maximal evalue considered\" />\n+\t\t\t\t<param name=\"ms_amanda_instrument\" label=\"MS Amanda: instrument\" type=\"float\" value=\"100\" help=\"MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.).\" />\n+\t\t\t\t<param name=\"ms_amanda_max_rank\" type=\"integer\" value=\"5\" \n+\t\t\t\t\tlabel=\"MS Amanda: Maximum Rank\" help=\"MS Amanda maximum rank\" />\n+\t\t\t\t<param name=\"ms_amanda_mono\" type=\"boolean\" truevalue=\"1\" falsevalue=\"0\" checked=\"true\"\n+\t\t\t\t\tlabel=\"MS Amanda: Use Monoisotopic Mass Values\" help=\"MS Amanda use monoisotopic mass values\" />\n+            </when>\n+        </conditional>\n+\t\t\n+-->\n+\t\t<!-- TIDE ADVANCED PARAMETERS -->\n+        <conditional name=\"tide\">\n+            <param name=\"tide_advanced\" type=\"select\" label=\"TIDE Options\">\n+                <option value=\"yes\">Advanced</option>\n+                <option value=\"no\" selected=\"True\">Default</option>\n+            </param>\n+            <when value=\"no\" />\n+            <when value=\"yes\">\n+                <param name=\"tide_num_ptms\" type=\"integer\" value=\"100\"\n+                    label=\"TIDE: Maximum Number of PTMs\" help=\"Set the maximum number of PTMs on peptide to be considered\"/>\n+                <param name=\"tide_num_ptms_per_type\" type=\"integer\" value=\"2\"\n+                    label=\"TIDE: Maximum Number of PTMs of each Type\" help=\"Set the maximum number of PTMs of each type to be considered\"/>\n+                <param name=\"tide_min_pep_length\" type=\"integer\" value=\"6\"\n+                    label=\"TIDE: Minimum Peptide Length\" help=\"Set the minimum length of peptide to be considered\"/>\n+                <param name=\"tide_max_pep_length\" type=\"integer\" value=\"30\"\n+                    label=\"TIDE: Maximum Peptide Length\" help=\"Set the maximum length of peptide to be considered\"/>\n+                <param name=\"tide_min_prec_mass\" type=\"float\" value=\"200.0\"\n+                    label=\"TIDE: Minimum Precursor Mass\" help=\"Set the minimum precursor mass to be considered\"/>\n+                <param name=\"tide_max_prec_mass\" type=\"float\" value=\"7200.0\"\n+                    label=\"TIDE: Maximum Precursor Mass\" help=\"Set the maximum precursor mass to be considered\"/>\n+  \t<param name=\"tide_decoy_format\" label=\"TIDE: Decoy Format\" type=\"select\" help=\"Select the format for generating the decoy sequences\">\n+\t\t\t                \t<option value=\"none\" selected=\"True\">none</option>\n+\t\t\t                \t<option value=\"shuffle\" >shuffle</option>\n+\t\t\t                \t<option value=\"peptide-revers\" >peptide-reverse</option>\n+\t\t\t                \t<option value=\"protein-reverse\" >protein-reverse</option>\n+\t</param>\n+  \t<param name=\"tide_keep_terminals\" label=\"TIDE: Keep Terminals\" type=\"select\" help=\"Select to keep the terminal amino acids when creating decoys\">\n+\t\t\t                \t<option value=\"N\" >N</option>\n+\t\t\t                \t<option value=\"C\" >C</option>\n+\t\t\t                \t<option value=\"NC\" selected=\"True\">NC</option>\n+\t\t\t                \t<option value=\"non\" >none</option>\n+\t</param>\n+                <param name=\"tide_decoy_seed\" type=\"integer\" value=\"1\"\n+                    label=\"TIDE: Decoy Seed\" help=\"Set the decoy seed\"/>\n+                <param name=\"tide_output_folder\" type=\"text\" value=\"crux-output\"","path":"tools/peptideshaker/searchgui.xml","position":769,"original_position":769,"commit_id":"990a3b0d8c960c653ce294d0312dc0768fff9ca3","original_commit_id":"990a3b0d8c960c653ce294d0312dc0768fff9ca3","user":{"login":"bgruening","id":469983,"avatar_url":"https://avatars.githubusercontent.com/u/469983?v=3","gravatar_id":"","url":"https://api.github.com/users/bgruening","html_url":"https://github.com/bgruening","followers_url":"https://api.github.com/users/bgruening/followers","following_url":"https://api.github.com/users/bgruening/following{/other_user}","gists_url":"https://api.github.com/users/bgruening/gists{/gist_id}","starred_url":"https://api.github.com/users/bgruening/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgruening/subscriptions","organizations_url":"https://api.github.com/users/bgruening/orgs","repos_url":"https://api.github.com/users/bgruening/repos","events_url":"https://api.github.com/users/bgruening/events{/privacy}","received_events_url":"https://api.github.com/users/bgruening/received_events","type":"User","site_admin":false},"body":"We probably don't want to display this to the user.","created_at":"2015-05-23T12:14:57Z","updated_at":"2015-05-23T12:14:57Z","html_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/33#discussion_r30944430","pull_request_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/33","_links":{"self":{"href":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/comments/30944430"},"html":{"href":"https://github.com/galaxyproteomics/tools-galaxyp/pull/33#discussion_r30944430"},"pull_request":{"href":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/33"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/33","id":35717825,"html_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/33","diff_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/33.diff","patch_url":"https://github.com/galaxyproteomics/tools-galaxyp/pull/33.patch","issue_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/33","number":33,"state":"open","locked":false,"title":"pullrequest_searchgui","user":{"login":"gerbenm","id":7263648,"avatar_url":"https://avatars.githubusercontent.com/u/7263648?v=3","gravatar_id":"","url":"https://api.github.com/users/gerbenm","html_url":"https://github.com/gerbenm","followers_url":"https://api.github.com/users/gerbenm/followers","following_url":"https://api.github.com/users/gerbenm/following{/other_user}","gists_url":"https://api.github.com/users/gerbenm/gists{/gist_id}","starred_url":"https://api.github.com/users/gerbenm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gerbenm/subscriptions","organizations_url":"https://api.github.com/users/gerbenm/orgs","repos_url":"https://api.github.com/users/gerbenm/repos","events_url":"https://api.github.com/users/gerbenm/events{/privacy}","received_events_url":"https://api.github.com/users/gerbenm/received_events","type":"User","site_admin":false},"body":"Björn, Ira,\r\n\r\nWe (Elvis and I) merged our SearchGUI tool wrapper with yours.\r\nLet me know your thoughts on that,\r\nRegards,\r\nGr.ben","created_at":"2015-05-19T10:53:45Z","updated_at":"2015-05-23T12:14:57Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/33/commits","review_comments_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/33/comments","review_comment_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/pulls/comments{/number}","comments_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/issues/33/comments","statuses_url":"https://api.github.com/repos/galaxyproteomics/tools-galaxyp/statuses/990a3b0d8c960c653ce294d0312dc0768fff9ca3","head":{"label":"gerbenm:master","ref":"master","sha":"990a3b0d8c960c653ce294d0312dc0768fff9ca3","user":{"login":"gerbenm","id":7263648,"avatar_url":"https://avatars.githubusercontent.com/u/7263648?v=3","gravatar_id":"","url":"https://api.github.com/users/gerbenm","html_url":"https://github.com/gerbenm","followers_url":"https://api.github.com/users/gerbenm/followers","following_url":"https://api.github.com/users/gerbenm/following{/other_user}","gists_url":"https://api.github.com/users/gerbenm/gists{/gist_id}","starred_url":"https://api.github.com/users/gerbenm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gerbenm/subscriptions","organizations_url":"https://api.github.com/users/gerbenm/orgs","repos_url":"https://api.github.com/users/gerbenm/repos","events_url":"https://api.github.com/users/gerbenm/events{/privacy}","received_events_url":"https://api.github.com/users/gerbenm/received_events","type":"User","site_admin":false},"repo":{"id":31884941,"name":"tools-galaxyp","full_name":"gerbenm/tools-galaxyp","owner":{"login":"gerbenm","id":7263648,"avatar_url":"https://avatars.githubusercontent.com/u/7263648?v=3","gravatar_id":"","url":"https://api.github.com/users/gerbenm","html_url":"https://github.com/gerbenm","followers_url":"https://api.github.com/users/gerbenm/followers","following_url":"https://api.github.com/users/gerbenm/following{/other_user}","gists_url":"https://api.github.com/users/gerbenm/gists{/gist_id}","starred_url":"https://api.github.com/users/gerbenm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gerbenm/subscriptions","organizations_url":"https://api.github.com/users/gerbenm/orgs","repos_url":"https://api.github.com/users/gerbenm/repos","events_url":"https://api.github.com/users/gerbenm/events{/privacy}","received_events_url":"https://api.github.com/users/gerbenm/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/gerbenm/tools-galaxyp","description":"Galaxy 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