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Fixed outstanding bugs in CTD tool (Human Genome Variation)

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H: Enter commit message.  Lines beginning with 'HG:' are removed.
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Richard Burhans
2011-09-26 15:56:01 -04:00
parent ef2688868c
commit 3f0fa2f6eb
2 changed files with 25 additions and 36 deletions
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tools/human_genome_variation/ctd.pl
+4 -4
View File
@@ -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 @@ my @form = ('inputType', $type, 'inputTerms', $d, 'report', $resType,
if ($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');
tools/human_genome_variation/ctd.xml
+21 -32
View File
@@ -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>