1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2e6b536c797f/ changeset: 2e6b536c797f user: richard_burhans date: 2011-09-26 21:56:01 summary: Fixed outstanding bugs in CTD tool (Human Genome Variation) H: Enter commit message. Lines beginning with 'HG:' are removed. affected #: 2 files (-1 bytes) --- a/tools/human_genome_variation/ctd.pl Mon Sep 26 15:29:19 2011 -0400 +++ b/tools/human_genome_variation/ctd.pl Mon Sep 26 15:56:01 2011 -0400 @@ -1,8 +1,5 @@ -#!/usr/bin/env perl - +#!/usr/bin/perl -w use strict; -use warnings; - use LWP::UserAgent; require HTTP::Cookies; @@ -54,6 +51,9 @@ if ($resType eq 'cgixns') { #only add if this type push(@form, 'actionTypes', $actType); } +if ($resType eq 'go' or $resType eq 'go_enriched') { + push(@form, 'ontology', 'go_bp', 'ontology', 'go_mf', 'ontology', 'go_cc'); +} my $ua = LWP::UserAgent->new; $ua->cookie_jar(HTTP::Cookies->new( () )); $ua->agent('Mozilla/5.0'); --- a/tools/human_genome_variation/ctd.xml Mon Sep 26 15:29:19 2011 -0400 +++ b/tools/human_genome_variation/ctd.xml Mon Sep 26 15:56:01 2011 -0400 @@ -1,7 +1,7 @@ <tool id="ctdBatch_1" name="CTD" version="1.0.0"><description>analysis of chemicals, diseases, or genes</description><command interpreter="perl">#if $inType.inputType=="disease" #ctd.pl $input $numerical_column $inType.inputType $inType.report ANY $out_file1 -#else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report $inType.reportType.actType $out_file1 +#else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report "$inType.reportType.actType" $out_file1 #else #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report ANY $out_file1 #end if</command><inputs> @@ -18,14 +18,13 @@ <param name="report" label="Data to extract" type="select"><option value="cgixns">Curated chemical-gene interactions</option><option value="genes">Curated gene associations</option> - <option value="pathways">Pathway associations</option> + <option value="pathways_inferred">Inferred pathway associations</option> + <option value="pathways_enriched">Enriched pathway associations</option><option value="diseases" selected="true">All disease relationships</option><option value="diseases_curated"> Curated disease relationships only</option><option value="diseases_inferred"> Inferred disease relationships only</option><option value="go">All GO associations</option> - <option value="go_p"> GO biological Processes only</option> - <option value="go_f"> GO molecular Functions only</option> - <option value="go_c"> GO cellular Components only</option> + <option value="go_enriched">Enriched GO associations only</option></param><when value="genes"><!-- do nothing --> @@ -33,6 +32,12 @@ <when value="pathways"><!-- do nothing --></when> + <when value="pathways_curated"> + <!-- do nothing --> + </when> + <when value="pathways_inferred"> + <!-- do nothing --> + </when><when value="diseases"><!-- do nothing --></when> @@ -45,13 +50,7 @@ <when value="go"><!-- do nothing --></when> - <when value="go_p"> - <!-- do nothing --> - </when> - <when value="go_f"> - <!-- do nothing --> - </when> - <when value="go_c"> + <when value="go_enriched"><!-- do nothing --></when><when value="cgixns"> @@ -117,30 +116,29 @@ <when value="disease"><param name="report" label="Data to extract" type="select"><option value="chems">Chemical associations</option> - <option value="chems_direct">Chemical associations direct relationships only</option> - <option value="chems_inferred">Chemical associations inferred relationships only</option> - <option value="genes">Curated gene associations</option> - <option value="pathways">Pathway associations</option> + <option value="chems_curated">Curated chemical associations only</option> + <option value="chems_inferred">Inferred chemical associations only</option> + <option value="genes">Gene associations</option> + <option value="genes_curated">Curated gene associations</option> + <option value="genes_inferred">Inferred gene associations</option> + <option value="pathways_inferred">Inferred pathway associations</option></param></when><when value="gene"><conditional name='reportType'><param name="report" label="Data to extract" type="select"><option value="cgixns">Curated chemical-gene interactions</option> - <option value="chems">Curated chemical associations</option> - <option value="pathways">Pathway associations</option> + <option value="chems_curated">Curated chemical associations</option> + <option value="pathways_curated">Curated pathway associations</option><option value="diseases" selected="true">All disease relationships</option><option value="diseases_curated"> Curated disease relationships only</option><option value="diseases_inferred"> Inferred disease relationships only</option><option value="go">All GO associations</option> - <option value="go_p"> GO biological Processes only</option> - <option value="go_f"> GO molecular Functions only</option> - <option value="go_c"> GO cellular Components only</option></param> - <when value="chems"> + <when value="chems_curated"><!-- do nothing --></when> - <when value="pathways"> + <when value="pathways_curated"><!-- do nothing --></when><when value="diseases"> @@ -155,15 +153,6 @@ <when value="go"><!-- do nothing --></when> - <when value="go_p"> - <!-- do nothing --> - </when> - <when value="go_f"> - <!-- do nothing --> - </when> - <when value="go_c"> - <!-- do nothing --> - </when><when value="cgixns"><param name="actType" label="Interaction type" type="select"><option value="ANY">ANY</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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