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comparison varextract.xml @ 23:5db0545b9004 draft

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update to v0.1.7.3
author wolma
date Thu, 21 Jul 2016 03:55:49 -0400
parents c46406466625
children
comparison
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22:24154c580718 23:5db0545b9004
1 <tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.2"> 1 <tool id="extract_variants" name="Extract Variant Sites" version="0.1.7.3">
2 <description>from a BCF file</description> 2 <description>from a BCF file</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements" />
7 <version_command>python3 -m MiModD version -q</version_command> 7 <version_command>python3 -m MiModD version -q</version_command>
8 <command> 8 <command>
9 python3 -m MiModD varextract "$ifile" 9 python3 -m MiModD varextract "$ifile"
10 #if $len($sitesinfo) 10 #if $len($sitesinfo)
11 -p 11 -p
12 #for $source in $sitesinfo 12 #for $source in $sitesinfo
13 "${source.pre_vcf}" 13 "${source.pre_vcf}"
17 $keep_alts 17 $keep_alts
18 --verbose 18 --verbose
19 </command> 19 </command>
20 20
21 <inputs> 21 <inputs>
22 <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate the input for this tool."/> 22 <param format="bcf" help="Use the Variant Calling tool to generate the input for this tool." label="BCF input file" name="ifile" type="data" />
23 <repeat name="sitesinfo" title="include information from pre-calculated vcf file" default="0"> 23 <repeat default="0" name="sitesinfo" title="include information from pre-calculated vcf file">
24 <param name="pre_vcf" type="data" format="vcf" label="independently generated vcf file" /> 24 <param format="vcf" label="independently generated vcf file" name="pre_vcf" type="data" />
25 </repeat> 25 </repeat>
26 <param name="keep_alts" type="boolean" label="keep all sites with alternate bases" truevalue="-a" falsevalue="" checked="false" help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." /> 26 <param checked="false" falsevalue="" help="If selected, the VCF output will include ALL sites for which non-reference bases have been observed, i.e., even those not considered allelic sites by the variant caller." label="keep all sites with alternate bases" name="keep_alts" truevalue="-a" type="boolean" />
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="output_vcf" format="vcf" label="Variants extracted with MiModd from ${on_string}"/> 29 <data format="vcf" label="Variants extracted with MiModd from ${on_string}" name="output_vcf" />
30 </outputs> 30 </outputs>
31 31
32 <help> 32 <help>
33 .. class:: infomark 33 .. class:: infomark
34 34