{"action":"created","comment":{"url":"https://api.github.com/repos/bgruening/galaxytools/pulls/comments/38265993","id":38265993,"diff_hunk":"@@ -0,0 +1,286 @@\n+<tool id=\"quast\" name=\"Quast\" version=\"3.0\">\n+    <description>QUality ASsessment Tool for Genome Assemblies</description>\n+    <macros>\n+        <token name=\"@EXECUTABLE@\">RNAshapes</token>\n+            <macro name=\"macro-meta_reference\">\n+                <param name=\"meta_reference\" type=\"data\" format=\"fasta\"\n+                    label=\"Reference file (optional)\"\n+                    optional=\"true\" multiple=\"true\" \n+                    help=\"Accepts multiple fasta files with multiple sequences each (FASTA format)\"/>\n+            </macro>\n+            <macro name=\"macro-eupro_reference\">\n+                <param name=\"eupro_reference\" type=\"data\" format=\"fasta\"    \n+                    label=\"Reference file (optional)\"\n+                    optional=\"true\" multiple=\"false\" \n+                    help=\"Accepts one reference file (FASTA format)\"/>\n+            </macro>\n+    </macros>\n+    <requirements>\n+    </requirements>\n+    <stdio>\n+        <exit_code range=\"1:\" level=\"fatal\" description=\"Error occurred. Please check Tool Standard Error\" />\n+        <exit_code range=\":-1\" level=\"fatal\" description=\"Error occurred. Please check Tool Standard Error\" />\n+    </stdio>\n+    <version_command>Quast --version</version_command>\n+    <command><![CDATA[\n+        #if $organism_type.organism=='meta':\n+            metaquast.py\n+            ##-R $organism_type.meta_reference\n+            #if $organism_type.meta_reference is not None:\n+               -R #echo ','.join(['\"%s\"' % $ref for $ref in $organism_type.meta_reference])#\n+            #end if\n+            --output-dir ./out\n+        #else:\n+            quast.py\n+            #if $organism_type.eupro_reference:\n+                -R $organism_type.eupro_reference\n+            #end if\n+            --output-dir ./out\n+        #end if\n+        --min-contig $min_contig\n+        $scaffolds\n+        #if $genes.find_genes:\n+            $genes.find_genes\n+            #if $organism_type.organism==\"eukaryote\":\n+                --eukaryote\n+            #end if\n+            #if $organism_type.organism==\"meta\":\n+                --meta\n+            #end if\n+            #if $genes.gene_coordinates:\n+                -G $genes.gene_coordinates\n+            #end if\n+            #if $genes.operon_coordinates:\n+                -O $genes.operon_coordinates\n+            #end if\n+        #end if\n+        #for $file in $fasta_input:\n+            '$file'\n+        #end for\n+        #if $organism_type.organism==\"meta\":\n+            &&\n+            mv ./out/combined_quast_output/report.html $html 2> /dev/null\n+            \n+            ## move aux files to accessible directory\n+            &&\n+            mkdir -p $html.files_path 2> /dev/null\n+            &&\n+            mv ./out/combined_quast_output/report_html_aux $html.files_path 2> /dev/null\n+        #end if\n+    ]]></command>\n+    <inputs>\n+        <conditional name=\"organism_type\">\n+            <param name=\"organism\" type=\"select\" label=\"Data files are:\">\n+                 <option value=\"\">prokaryotic</option>\n+                 <option value=\"eukaryote\">eukaryotic</option>\n+                 <option value=\"meta\">metagenome</option>\n+            </param>\n+            <when value =\"meta\">\n+                 <expand macro=\"macro-meta_reference\"/>\n+            </when>\n+            <when value =\"eukaryote\">\n+                 <expand macro=\"macro-eupro_reference\"/>\n+            </when>\n+            <when value =\"\">\n+                 <expand macro=\"macro-eupro_reference\"/>\n+            </when>\n+        </conditional>\n+        <param name=\"fasta_input\" multiple=\"True\" type=\"data\" format=\"fasta\" label=\"Alignment file(s)\"/>\n+        <param name=\"min_contig\" type=\"integer\" size=\"20\" value=\"500\" label=\"Skip contigs shorter than x bp\"/>\n+        <param name=\"scaffolds\" type=\"boolean\" checked=\"false\" truevalue=\"--scaffolds\" falsevalue=\"\"\n+            label=\"Split scaffolds?\"\n+            help=\"The assemblies are scaffolds (rather than contigs).\n+                QUAST will add split versions of assemblies to the comparison.\n+                Assemblies are split by continuous fragments of N's of length >= 10.\" />\n+        <conditional name=\"genes\">\n+            <param name=\"find_genes\" type=\"select\" label=\"Find genes?\" \n+                    help=\"Prokaryotic (find genes with GenemarkS, process circular chromosomes), Eukaryotic (find genes with GlimmerHMM), Metagenome (use MetaGeneMark for gene prediction)\">\n+                 <option value=\"\">No</option>\n+                <option value=\"--gene-finding\">Yes</option>\n+            </param>\n+            <when value=\"--gene-finding\">\n+                    <param name=\"gene_coordinates\" type=\"data\" format=\"gff\" optional=\"true\" multiple=\"false\"\n+                        label=\"Gene coordinates in the reference (optional)\" />\n+                    <param name=\"operon_coordinates\" type=\"data\" format=\"gff\" optional=\"true\" multiple=\"false\"\n+                        label=\"Operon coordinates in the reference (optional)\" />\n+            </when>\n+        </conditional>\n+    </inputs>\n+    <outputs>\n+        <data name=\"outfile\" format=\"pdf\" from_work_dir=\"./out/combined_quast_output/report.pdf\" />\n+        <data name=\"outfile2\" format=\"tabular\" from_work_dir=\"./out/combined_quast_output/report.txt\"/>\n+        <data name=\"html\" format=\"html\" label=\"${tool.name} on ${on_string} (html report)\"/>\n+    </outputs>\n+    <tests>\n+        <test>\n+            <param name=\"organism\" value=\"meta\"/>\n+            <param name=\"fasta_input\" value=\"meta_contigs_1.fasta,meta_contigs_2.fasta\" />\n+            <param name=\"meta_reference\" value=\"meta_ref_3.fasta,meta_ref_2.fasta\" />\n+            <output name=\"outfile\" file=\"report_4.pdf\" ftype=\"pdf\" compare=\"sim_size\"/>\n+            <output name=\"outfile2\" file=\"report_4.txt\" ftype=\"tabular\" compare=\"sim_size\"/>\n+            <output name=\"html\" file=\"report_4.html\" ftype=\"html\" compare=\"sim_size\"/>\n+        </test>\n+        <test>\n+            <param name=\"organism\" value=\"\" />\n+            <param name=\"fasta_input\" value=\"reference.fasta.gz\" />\n+            <param name=\"scaffolds\" value=\"!!!!!!!!!scaffolds\" 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