Mercurial > repos > gandres > vcftools_filter_stats_diversity

comparison VCFToolFilter/vcfToolsFilter.xml @ 3:612066e3f57d draft

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author gandres
date Mon, 09 Nov 2015 05:18:45 -0500
parents ac7c9e40d601
children b762ecbe2314
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2:ac7c9e40d601 3:612066e3f57d
1 <tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.1"> 1 <tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.2">
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 -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">perl</requirement> 8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="0.1.12b">vcftools</requirement> 9 <requirement type="package" version="0.1.12b">vcftools</requirement>
10 </requirements> 10 </requirements>
11 11
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> 12
13 <version_command> 13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
14 <!-- 14 <stdio>
15 tool_binary -v 15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
16 --> 16 <exit_code range="1:" level="fatal" />
17 </version_command> 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_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end 21 vcfToolsFilter.sh $filein $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
53 </param> 53 </param>
54 <param name="frequency" type="float" value="0.001" label="Minimum MAF." help="Minimum frequency." /> 54 <param name="frequency" type="float" value="0.001" label="Minimum MAF." help="Minimum frequency." />
55 <param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." /> 55 <param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." />
56 <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." /> 56 <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />
57 <param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" /> 57 <param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" />
58 <param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" /> 58 <param name="nb_alleles_max" type="integer" value="4" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" />
59 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." > 59 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
60 <option value="ALL" selected="true">All</option> 60 <option value="ALL" selected="true">All</option>
61 <option value="SNP">SNP</option> 61 <option value="SNP">SNP</option>
62 <option value="INDEL">Indel</option> 62 <option value="INDEL">Indel</option>
63 </param> 63 </param>
71 <change_format> 71 <change_format>
72 <when input="export" value="freq" format="tabular" /> 72 <when input="export" value="freq" format="tabular" />
73 <when input="export" value="plink" format="txt" /> 73 <when input="export" value="plink" format="txt" />
74 </change_format> 74 </change_format>
75 </data> 75 </data>
76 <data name="fileout_map" format="txt" label="${fileout_label}.map"> 76 <data name="fileout_map" format="tabular" label="${fileout_label}.map">
77 <filter>(export == 'plink')</filter> 77 <filter>(export == 'plink')</filter>
78 </data> 78 </data>
79 <data name="filelog" format="txt" label="${fileout_label}.log" /> 79 <data name="filelog" format="txt" label="${fileout_label}.log" />
80 </outputs> 80 </outputs>
81 81
82 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
83 <stdio>
84 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
85 <exit_code range="1:" level="fatal" />
86 </stdio>
87 82
88 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 83 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
89 <tests> 84 <tests>
90 <!-- [HELP] Test files have to be in the ~/test-data directory --> 85 <!-- [HELP] Test files have to be in the ~/test-data directory -->
91 <test> 86 <test>
99 <param name="nb_alleles_max" value="4" /> 94 <param name="nb_alleles_max" value="4" />
100 <param name="type_p" value="ALL" /> 95 <param name="type_p" value="ALL" />
101 <param name="bound_start" value="1" /> 96 <param name="bound_start" value="1" />
102 <param name="bound_end" value="100000000" /> 97 <param name="bound_end" value="100000000" />
103 <output name="fileout" file="result.vcf" /> 98 <output name="fileout" file="result.vcf" />
104 <output name="filelog" file="result.log" /> 99 </test>
100 <test>
101 <param name="filein" value="sample.vcf" />
102 <param name="export" value="plink" />
103 <param name="type_p" value="SNP" />
104 <output name="fileout" file="result.ped" />
105 <output name="fileout_map" file="result.map" />
106 </test>
107 <test>
108 <param name="filein" value="sample.vcf" />
109 <param name="export" value="freq" />
110 <param name="type_p" value="ALL" />
111 <output name="fileout" file="result.frq" />
105 </test> 112 </test>
106 </tests> 113 </tests>
107 114
108 <!-- [OPTIONAL] Help displayed in Galaxy --> 115 <!-- [OPTIONAL] Help displayed in Galaxy -->
109 <help> 116 <help>