{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/pulls/comments/25370118","id":25370118,"diff_hunk":"@@ -0,0 +1,310 @@\n+<tool id=\"velvetg\" name=\"velvetg\" version=\"1.0.0\">\n+  <description>Velvet sequence assembler for very short reads</description>\n+  <version_command>velvetg 2&gt;&amp;1 | grep \"Version\" | sed -e 's/Version //'</version_command>\n+  <requirements>\n+      <requirement type=\"package\" version=\"1.2.10\">velvet</requirement>\n+  </requirements>\n+  <stdio>\n+      <exit_code range=\"1:\" />\n+      <exit_code range=\":-1\" />\n+      <regex match=\"Error:\" />\n+      <regex match=\"Exception:\" />\n+  </stdio>\n+  <command interpreter=\"python\">\n+    velvetg_wrapper.py\n+           '$input.extra_files_path'\n+           #if $generate_amos.afg  == \"yes\":\n+               -amos_file $generate_amos.afg\n+           #end if\n+           #if $unused_reads.generate_unused  == \"yes\":\n+               -unused_reads $unused_reads.generate_unused\n+           #end if\n+           $read_trkg\n+           #if $coverage.cutoff == \"auto\":\n+               -cov_cutoff auto\n+           #elif $coverage.cutoff == \"value\":\n+               -cov_cutoff $coverage.cov_cutoff\n+           #end if\n+           #if $expected.coverage == \"auto\":\n+               -exp_cov auto\n+           #elif $expected.coverage == \"value\":\n+               -exp_cov $expected.exp_cov\n+           #end if\n+           #if $contig_lgth.use_contig_lgth == \"yes\":\n+               -min_contig_lgth $contig_lgth.min_contig_lgth\n+           #end if\n+           #if $reads.paired == \"yes\":\n+               #if int($reads.ins_length) > 0:\n+                   -ins_length $reads.ins_length\n+               #end if\n+               #if $reads.options.advanced == \"yes\":\n+                   #if int($reads.options.ins_length_sd) > 0:\n+                       -ins_length_sd $reads.options.ins_length_sd\n+                   #end if\n+                   #if int($reads.options.ins_length2) > 0:\n+                       -ins_length2 $reads.options.ins_length2\n+                   #end if\n+                   #if int($reads.options.ins_length2_sd) > 0:\n+                       -ins_length2_sd $reads.options.ins_length2_sd\n+                   #end if\n+                   #if int($reads.options.ins_length_long) > 0:\n+                       -ins_length_long $reads.options.ins_length_long\n+                   #end if\n+                   #if int($reads.options.ins_length_long_sd) > 0:\n+                       -ins_length_long_sd $reads.options.ins_length_long_sd\n+                   #end if\n+                   #if int($reads.options.max_branch_length) > 0:\n+                       -max_branch_length $reads.options.max_branch_length\n+                   #end if\n+                   #if int($reads.options.max_divergence) > 0:\n+                       -max_divergence $reads.options.max_divergence\n+                   #end if\n+                   #if int($reads.options.max_gap_count) > 0:\n+                       -max_gap_count $reads.options.max_gap_count\n+                   #end if\n+                   #if int($reads.options.min_pair_count) > 0:\n+                       -min_pair_count $reads.options.min_pair_count\n+                   #end if\n+                   #if int($reads.options.max_coverage) > 0:\n+                       -max_coverage $reads.options.max_coverage\n+                   #end if\n+                   #if int($reads.options.long_mult_cutoff) > 0:\n+                       -long_mult_cutoff $reads.options.long_mult_cutoff\n+                   #end if\n+                   $reads.options.scaffolding\n+               #end if\n+           #end if\n+  </command>\n+  <inputs>\n+    <param name=\"input\" type=\"data\" format=\"velvet\" label=\"Velvet Dataset\" help=\"Prepared by velveth.\"/>\n+    <conditional name=\"generate_amos\">\n+      <param name=\"afg\" type=\"select\" label=\"Generate a AMOS.afg file\">\n+        <option value=\"no\">No</option>\n+        <option value=\"yes\">Yes</option>\n+      </param>\n+      <when value=\"no\"/>\n+      <when value=\"yes\"/>\n+    </conditional>\n+\n+    <conditional name=\"unused_reads\">\n+      <param name=\"generate_unused\" type=\"select\" label=\"Generate a UnusedReads fasta file\">\n+        <option value=\"no\">No</option>\n+        <option value=\"yes\">Yes</option>\n+      </param>\n+      <when value=\"no\"/>\n+      <when value=\"yes\"/>\n+    </conditional>\n+\n+    <conditional name=\"last_graph\">\n+      <param name=\"generate_graph\" type=\"select\" label=\"Generate velvet LastGraph file\">\n+        <option value=\"no\">No</option>\n+        <option value=\"yes\">Yes</option>\n+      </param>\n+      <when value=\"no\"/>\n+      <when value=\"yes\"/>\n+    </conditional>\n+\n+    <param name=\"read_trkg\" type=\"boolean\" checked=\"false\" truevalue=\"-read_trkg yes\" falsevalue=\"-read_trkg no\" label=\"Tracking of short read positions in assembly\" help=\"Generates Graph2 dataset\" />\n+\n+    <conditional name=\"coverage\">\n+      <param name=\"cutoff\" type=\"select\" label=\"Coverage cutoff\" help=\"\">\n+        <option value=\"none\">None</option>\n+        <option value=\"auto\">Automatically Determined</option>\n+        <option value=\"value\">Specify Cutoff Value</option>\n+      </param>\n+      <when value=\"none\"/>\n+      <when value=\"auto\"/>\n+      <when value=\"value\">\n+        <param name=\"cov_cutoff\" value = \"10.0\" label=\"Remove nodes with coverage below\" type=\"float\" />\n+      </when>\n+    </conditional>\n+\n+    <conditional name=\"expected\">\n+      <param name=\"coverage\" type=\"select\" label=\"Expected Coverage of Unique Regions\" help=\"\">\n+        <option value=\"none\">None</option>\n+        <option value=\"auto\">Automatically Determined</option>\n+        <option value=\"value\">Specify Expected Value</option>\n+      </param>\n+      <when value=\"none\"/>\n+      <when value=\"auto\"/>\n+      <when value=\"value\">\n+        <param name=\"exp_cov\" value = \"10.0\" label=\"Remove nodes with coverage below\" type=\"float\" />\n+      </when>\n+    </conditional>\n+\n+    <conditional name=\"contig_lgth\">\n+      <param name=\"use_contig_lgth\" type=\"select\" label=\" Set minimum contig length\" help=\"minimum contig length exported to contigs.fa file (default: hash length * 2).\">\n+        <option value=\"no\">No</option>\n+        <option value=\"yes\">Yes</option>\n+      </param>\n+      <when value=\"no\"/>\n+      <when value=\"yes\">\n+        <param name=\"min_contig_lgth\" value = \"42\" label=\"minimum contig length\" type=\"integer\" help=\"minimum contig length exported to contigs.fa file (default: hash length * 2)\"/>\n+      </when>\n+    </conditional>\n+\n+    <conditional name=\"reads\">\n+      <param name=\"paired\" type=\"select\" label=\"Using Paired Reads\">\n+        <option value=\"no\">No</option>\n+        <option value=\"yes\" selected=\"${input.metadata.paired_end_reads}\">Yes</option>\n+      </param>\n+      <when value=\"no\"/>\n+      <when value=\"yes\">\n+        <param name=\"ins_length\" value = \"-1\" label=\"Insert Length in Paired-End Read dataset (ignored when -1)\" type=\"integer\" help=\"Expected distance between two paired end reads\"/>\n+        <conditional name=\"options\">\n+          <param name=\"advanced\" type=\"select\" label=\"Velvet Advanced Options\">\n+            <option value=\"no\">Use Defaults</option>\n+            <option value=\"yes\">Set Advanced Option Values</option>\n+          </param>\n+          <when value=\"no\"/>\n+          <when value=\"yes\">\n+            <param name=\"ins_length_sd\" value = \"-1\" label=\"Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)\" type=\"integer\" help=\"Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)\"/>\n+            <param name=\"ins_length2\" value = \"-1\" label=\"Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)\" type=\"integer\" help=\"Expected distance between two paired end reads in the second short-read dataset\"/>","path":"tools/velvet/velvetg.xml","position":162,"original_position":162,"commit_id":"d3956afd504efb5f96eec476e4db008a915bc326","original_commit_id":"d3956afd504efb5f96eec476e4db008a915bc326","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":"The spaces between `value` and `=` should be removed.","created_at":"2015-02-25T19:26:26Z","updated_at":"2015-02-25T19:26:26Z","html_url":"https://github.com/galaxyproject/tools-devteam/pull/64#discussion_r25370118","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-devteam/pulls/64","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-devteam/pulls/comments/25370118"},"html":{"href":"https://github.com/galaxyproject/tools-devteam/pull/64#discussion_r25370118"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-devteam/pulls/64"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-devteam/pulls/64","id":29937184,"html_url":"https://github.com/galaxyproject/tools-devteam/pull/64","diff_url":"https://github.com/galaxyproject/tools-devteam/pull/64.diff","patch_url":"https://github.com/galaxyproject/tools-devteam/pull/64.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-devteam/issues/64","number":64,"state":"open","locked":false,"title":"Velvet (+package) from galaxy","user":{"login":"erasche","id":458683,"avatar_url":"https://avatars.githubusercontent.com/u/458683?v=3","gravatar_id":"","url":"https://api.github.com/users/erasche","html_url":"https://github.com/erasche","followers_url":"https://api.github.com/users/erasche/followers","following_url":"https://api.github.com/users/erasche/following{/other_user}","gists_url":"https://api.github.com/users/erasche/gists{/gist_id}","starred_url":"https://api.github.com/users/erasche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erasche/subscriptions","organizations_url":"https://api.github.com/users/erasche/orgs","repos_url":"https://api.github.com/users/erasche/repos","events_url":"https://api.github.com/users/erasche/events{/privacy}","received_events_url":"https://api.github.com/users/erasche/received_events","type":"User","site_admin":false},"body":"Imported the commented out sr_assembly tool velvet, added a package for it.\r\n\r\n*it would be nice* if Galaxy had configurable package installs as part of the future. It's, admittedly, a bit of a corner case, but velvet has the setting `MAXKMERLENGTH` which we need set higher than the default. Instead I just re-built the tool and copied the binaries manually into the install 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