Mercurial > repos > wolma > mimodd_cloudmap_prepare

comparison cloudmap.xml @ 1:e81a2448d1fb draft

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upgrade to v0.1.5.1
author wolma
date Fri, 16 Jan 2015 10:42:08 -0500
parents 17ea8fd2ca18
children dea4e23ba53f
comparison
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0:17ea8fd2ca18 1:e81a2448d1fb
1 <tool id="cloudmap_prepare" name="Prepare variant data for mapping"> 1 <tool id="cloudmap_prepare" name="Prepare variant data for mapping">
2 <description>with the CloudMap series of tools.</description> 2 <description>with the CloudMap series of tools.</description>
3 <requirements>
4 <requirement type="package" version="0.1.5">mimodd</requirement>
5 </requirements>
6 <version_command>mimodd version -q</version_command> 3 <version_command>mimodd version -q</version_command>
7 <command> 4 <command>
8 mimodd cloudmap "$ifile" ${run.mode} 5 mimodd cloudmap "$ifile" ${run.mode}
9 6
10 #if $str($run.mode) != "EMS": 7 #if $str($run.mode) != "SVD":
11 "${run.refsample}" 8 "${run.refsample}"
12 #end if 9 #end if
13 10
14 "$sample" -o $ofile 11 "$sample" -o $ofile
15 12
20 17
21 <inputs> 18 <inputs>
22 <param name="ifile" type="data" format="vcf" label="vcf input file" /> 19 <param name="ifile" type="data" format="vcf" label="vcf input file" />
23 <conditional name="run"> 20 <conditional name="run">
24 <param name="mode" type="select" label="CloudMap analysis to prepare data for"> 21 <param name="mode" type="select" label="CloudMap analysis to prepare data for">
25 <option value="EMS">EMS Variant Density Mapping</option> 22 <option value="SVD">EMS Variant Density Mapping</option>
26 <option value="VARIANT">Variant Discovery Mapping</option> 23 <option value="VAF">Variant Discovery / Hawaiian Variant Mapping</option>
27 <option value="HAWAIIAN">Hawaiian Variant Mapping</option>
28 </param> 24 </param>
29 <when value="EMS"> 25 <when value="SVD">
30 <param name="refsample" type="hidden" value="None" /> 26 <param name="refsample" type="hidden" value="None" />
31 </when> 27 </when>
32 <when value="VARIANT"> 28 <when value="VAF">
33 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be EXCLUDED from the analysis" /> 29 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides mapping strain variants" />
34 </when>
35 <when value="HAWAIIAN">
36 <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be INCLUDED in the analysis" />
37 </when> 30 </when>
38 </conditional> 31 </conditional>
39 <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" /> 32 <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
40 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" /> 33 <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />
41 34
42 </inputs> 35 </inputs>
43 36
44 <outputs> 37 <outputs>
45 <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" /> 38 <data name="ofile" format="vcf" label="CloudMap-ready ${run.mode} File from ${on_string}" />
46 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}"> 39 <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
47 <filter>seqdict</filter> 40 <filter>seqdict</filter>
48 </data> 41 </data>
49 </outputs> 42 </outputs>
50 43