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comparison check_gwas_inputs/CheckGWASInputs.xml @ 4:10627af23f10 draft

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planemo upload
author gandres
date Tue, 15 Dec 2015 05:18:02 -0500
parents 345f88a8f483
children ec22fcacb66c
comparison
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3:345f88a8f483 4:10627af23f10
1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1"> 1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0">
2 <description>checks concordance between input files for GWAS analysis</description> 2 <description>checks concordance between input files for GWAS analysis</description>
3
4 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
5 <requirements>
6 <requirement type="binary">perl</requirement>
7 </requirements>
8
9 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
10 <stdio>
11 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
12 <exit_code range="1:" level="fatal" />
13 </stdio>
14
3 <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats 15 <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats
4 </command> 16 </command>
5 <inputs> 17 <inputs>
6 <param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> 18 <param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
7 <param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/> 19 <param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/>
8 </inputs> 20 </inputs>
9 <outputs> 21 <outputs>
10 <data format="txt" name="out_hapmap" label="Hapmap output"/> 22 <data format="txt" name="out_hapmap" label="Hapmap output"/>
11 <data format="txt" name="out_trait" label="Trait output"/> 23 <data format="txt" name="out_trait" label="Trait output"/>
12 <data format="txt" name="stats" label="Logfile and statistics"/> 24 <data format="txt" name="stats" label="Logfile and statistics"/>
13 </outputs> 25 </outputs>
14 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
15 <stdio>
16 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
17 <exit_code range="1:" level="fatal" />
18 </stdio>
19 26
20 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 27 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
21 <tests> 28 <tests>
22 <!-- [HELP] Test files have to be in the ~/test-data directory --> 29 <!-- [HELP] Test files have to be in the ~/test-data directory -->
23 <!-- [HELP] Multiple tests can be defined with different parameters --> 30 <!-- [HELP] Multiple tests can be defined with different parameters -->
24 <!--
25 <test> 31 <test>
32 <param name="hapmap" value="gwas-hapmap" />
33 <param name="trait" value="gwas-trait" />
34 <output name="out_hapmap" file="gwas-result.hapmap" />
35 <output name="out_trait" file="gwas-result.trait" />
36 <output name="stats" file="gwas-result.stats" />
26 </test> 37 </test>
27 -->
28 </tests> 38 </tests>
29 <help> 39 <help>
30 40
31 <![CDATA[ 41 <![CDATA[
32 42