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/
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