Mercurial > repos > gandres > vcftools_filter_stats_diversity

comparison VCFToolsStats/vcfToolsStats.xml @ 3:612066e3f57d draft

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Uploaded
author gandres
date Mon, 09 Nov 2015 05:18:45 -0500
parents ac7c9e40d601
children b762ecbe2314
comparison
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2:ac7c9e40d601 3:612066e3f57d
1 <tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.0.0"> 1 <tool id="sniplay_vcftoolsstats" name="VCFtools Stats" version="1.1.0">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name --> 3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> </description> 4 <description> </description>
5 5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">perl</requirement> 8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="0.1.12b">vcftools</requirement> 9 <requirement type="package" version="0.1.12b">vcftools</requirement>
10 </requirements> 10 </requirements>
11 11
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> 12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <version_command> 13 <stdio>
14 <!-- 14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 tool_binary -v 15 <exit_code range="1:" level="fatal" />
16 --> 16 </stdio>
17 </version_command>
18 17
19 <!-- [REQUIRED] The command to execute --> 18 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="perl"> 19 <command interpreter="perl">
21 vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog 20 vcfToolsStats.sh $filein $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog
22 </command> 21 </command>
23 22
24 <!-- [REQUIRED] Input files and tool parameters --> 23 <!-- [REQUIRED] Input files and tool parameters -->
25 <inputs> 24 <inputs>
26 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> 25 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
33 <data name="fileout_het" format="txt" label="${fileout_label}.het" /> 32 <data name="fileout_het" format="txt" label="${fileout_label}.het" />
34 <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" /> 33 <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" />
35 <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" /> 34 <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" />
36 <data name="filelog" format="txt" label="${fileout_label}.log" /> 35 <data name="filelog" format="txt" label="${fileout_label}.log" />
37 </outputs> 36 </outputs>
38
39 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
40 <stdio>
41 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
42 <exit_code range="1:" level="fatal" />
43 </stdio>
44 37
45 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 38 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
46 <tests> 39 <tests>
47 <!-- [HELP] Test files have to be in the ~/test-data directory --> 40 <!-- [HELP] Test files have to be in the ~/test-data directory -->
48 <test> 41 <test>
49 <param name="filein" value="sample.vcf" /> 42 <param name="filein" value="sample.vcf" />
50 <output name="fileout_annot" file="result.annotation" /> 43 <output name="fileout_annot" file="result.annotation" />
51 <output name="fileout_het" file="result.het" /> 44 <output name="fileout_het" file="result.het" />
52 <output name="fileout_imiss" file="result.imiss" /> 45 <output name="fileout_imiss" file="result.imiss" />
53 <output name="fileout_sum" file="result.TsTv.summary" /> 46 <output name="fileout_sum" file="result.TsTv.summary" />
54 <output name="filelog" file="result.log" />
55 </test> 47 </test>
56 </tests> 48 </tests>
57 49
58 <!-- [OPTIONAL] Help displayed in Galaxy --> 50 <!-- [OPTIONAL] Help displayed in Galaxy -->
59 <help> 51 <help>