Mercurial > repos > gandres > vcftools_filter_stats_diversity
comparison VCFToolFilter/vcfToolsFilter.xml @ 6:1420a55ca72b draft
planemo upload
author | gandres |
---|---|
date | Mon, 21 Mar 2016 10:22:36 -0400 |
parents | b762ecbe2314 |
children |
comparison
equal
deleted
inserted
replaced
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> |