Mercurial > repos > gandres > vcftools_filter_stats_diversity
diff VCFToolFilter/vcfToolsFilter.xml @ 6:1420a55ca72b draft
planemo upload
author | gandres |
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date | Mon, 21 Mar 2016 10:22:36 -0400 |
parents | b762ecbe2314 |
children |
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--- a/VCFToolFilter/vcfToolsFilter.xml Mon Feb 15 11:29:42 2016 -0500 +++ b/VCFToolFilter/vcfToolsFilter.xml Mon Mar 21 10:22:36 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.2"> +<tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.2.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> </description> @@ -18,7 +18,7 @@ <!-- [REQUIRED] The command to execute --> <command interpreter="perl"> - vcfToolsFilter.sh $filein $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end + vcfToolsFilter.sh $input $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end #if str( $samples ) == "": 'None' #else @@ -35,17 +35,13 @@ '' #end if </command> - + <code file="find_indiv.py"/> <!-- [REQUIRED] Input files and tool parameters --> <inputs> - <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> + <param name="input" type="data" format="vcf" optional="false" label="VCF input" /> <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/> - <param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list"> - <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> - </param> - <param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list"> - <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> - </param> + <param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(input)" help="Samples to be analyzed." /> + <param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." /> <param name="export" type="select" label="Output format" > <option value="VCF" selected="true">VCF</option> <option value="freq">freq</option> @@ -84,7 +80,7 @@ <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> - <param name="filein" value="sample.vcf" /> + <param name="input" value="sample.vcf" /> <param name="chromosomes" value="chr1" /> <param name="export" value="VCF" /> <param name="frequency" value="0.001" /> @@ -98,14 +94,14 @@ <output name="fileout" file="filter-result.vcf" /> </test> <test> - <param name="filein" value="sample.vcf" /> + <param name="input" value="sample.vcf" /> <param name="export" value="plink" /> <param name="type_p" value="SNP" /> <output name="fileout" file="filter-result.ped" /> <output name="fileout_map" file="filter-result.map" /> </test> <test> - <param name="filein" value="sample.vcf" /> + <param name="input" value="sample.vcf" /> <param name="export" value="freq" /> <param name="type_p" value="ALL" /> <output name="fileout" file="filter-result.frq" />