Mercurial > repos > gandres > vcftools_filter_stats_diversity

comparison VCFToolFilter/vcfToolsFilter.xml @ 6:1420a55ca72b draft

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planemo upload
author gandres
date Mon, 21 Mar 2016 10:22:36 -0400
parents b762ecbe2314
children
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5:ff9c990466be 6:1420a55ca72b
1 <tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.2"> 1 <tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.2.0">
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 -->
16 <exit_code range="1:" level="fatal" /> 16 <exit_code range="1:" level="fatal" />
17 </stdio> 17 </stdio>
18 18
19 <!-- [REQUIRED] The command to execute --> 19 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="perl"> 20 <command interpreter="perl">
21 vcfToolsFilter.sh $filein $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end 21 vcfToolsFilter.sh $input $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end
22 #if str( $samples ) == "": 22 #if str( $samples ) == "":
23 'None' 23 'None'
24 #else 24 #else
25 $samples 25 $samples
26 #end if 26 #end if
33 $fileout_map 33 $fileout_map
34 #else 34 #else
35 '' 35 ''
36 #end if 36 #end if
37 </command> 37 </command>
38 38 <code file="find_indiv.py"/>
39 <!-- [REQUIRED] Input files and tool parameters --> 39 <!-- [REQUIRED] Input files and tool parameters -->
40 <inputs> 40 <inputs>
41 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> 41 <param name="input" type="data" format="vcf" optional="false" label="VCF input" />
42 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/> 42 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/>
43 <param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list"> 43 <param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(input)" help="Samples to be analyzed." />
44 <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> 44 <param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />
45 </param>
46 <param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list">
47 <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator>
48 </param>
49 <param name="export" type="select" label="Output format" > 45 <param name="export" type="select" label="Output format" >
50 <option value="VCF" selected="true">VCF</option> 46 <option value="VCF" selected="true">VCF</option>
51 <option value="freq">freq</option> 47 <option value="freq">freq</option>
52 <option value="plink">plink</option> 48 <option value="plink">plink</option>
53 </param> 49 </param>
82 78
83 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 79 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
84 <tests> 80 <tests>
85 <!-- [HELP] Test files have to be in the ~/test-data directory --> 81 <!-- [HELP] Test files have to be in the ~/test-data directory -->
86 <test> 82 <test>
87 <param name="filein" value="sample.vcf" /> 83 <param name="input" value="sample.vcf" />
88 <param name="chromosomes" value="chr1" /> 84 <param name="chromosomes" value="chr1" />
89 <param name="export" value="VCF" /> 85 <param name="export" value="VCF" />
90 <param name="frequency" value="0.001" /> 86 <param name="frequency" value="0.001" />
91 <param name="max_freq" value="0.5" /> 87 <param name="max_freq" value="0.5" />
92 <param name="allow_missing" value="1" /> 88 <param name="allow_missing" value="1" />
96 <param name="bound_start" value="1" /> 92 <param name="bound_start" value="1" />
97 <param name="bound_end" value="100000000" /> 93 <param name="bound_end" value="100000000" />
98 <output name="fileout" file="filter-result.vcf" /> 94 <output name="fileout" file="filter-result.vcf" />
99 </test> 95 </test>
100 <test> 96 <test>
101 <param name="filein" value="sample.vcf" /> 97 <param name="input" value="sample.vcf" />
102 <param name="export" value="plink" /> 98 <param name="export" value="plink" />
103 <param name="type_p" value="SNP" /> 99 <param name="type_p" value="SNP" />
104 <output name="fileout" file="filter-result.ped" /> 100 <output name="fileout" file="filter-result.ped" />
105 <output name="fileout_map" file="filter-result.map" /> 101 <output name="fileout_map" file="filter-result.map" />
106 </test> 102 </test>
107 <test> 103 <test>
108 <param name="filein" value="sample.vcf" /> 104 <param name="input" value="sample.vcf" />
109 <param name="export" value="freq" /> 105 <param name="export" value="freq" />
110 <param name="type_p" value="ALL" /> 106 <param name="type_p" value="ALL" />
111 <output name="fileout" file="filter-result.frq" /> 107 <output name="fileout" file="filter-result.frq" />
112 </test> 108 </test>
113 </tests> 109 </tests>