Mercurial > repos > iuc > bcftools_convert_from_vcf

comparison bcftools_convert_from_vcf.xml @ 5:f40133892dbe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
author iuc
date Thu, 13 Apr 2017 16:25:31 -0400
parents e6f4932ceb70
children 6c6b5c192e0c
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4:e6f4932ceb70 5:f40133892dbe
10 </xml> 10 </xml>
11 <xml name="macro_haploid2diploid"> 11 <xml name="macro_haploid2diploid">
12 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" 12 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false"
13 label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/> 13 label="convert haploid genotypes to diploid homozygotes" help="(\-\-haploid2diploid)"/>
14 </xml> 14 </xml>
15 <xml name="macro_sexinfo">
16 <conditional name="sex_info">
17 <param name="sex_info_src" type="select" label="sex column">
18 <help><![CDATA[
19 SampleName SexDesignation:
20 <br>MaleSample M
21 <br>FemaleSample F
22 ]]></help>
23 <option value="none">None</option>
24 <option value="history">designations from history dataset</option>
25 <option value="entry">designations from text input</option>
26 </param>
27 <when value="none"/>
28 <when value="history">
29 <param name="sex_info_file" type="data" format="tabular" label="per sample sex designation file"/>
30 </when>
31 <when value="entry">
32 <param name="sex_info_lines" type="text" area="True" label="per sample sex designation" >
33 <validator type="regex" message="sample M or F separated by TAB">^(\S+[ \t][MF](\n\S+[ \t][MF])*)$</validator>
34 <sanitizer sanitize="False"/>
35 </param>
36 </when>
37 </conditional>
38 </xml>
39 <token name="@SAMPLE_SEX@">
40 #if $convert.sex_info.sex_info_src == 'entry':
41 --sex "$entered_sex_file"
42 #elif $convert.sex_info.sex_info_src == 'history':
43 --sex "$convert.sex_info.sex_info_file"
44 #end if
45 </token>
15 </macros> 46 </macros>
16 <expand macro="requirements" /> 47 <expand macro="requirements" />
17 <expand macro="version_command" /> 48 <expand macro="version_command" />
18 <command detect_errors="aggressive"><![CDATA[ 49 <command detect_errors="aggressive"><![CDATA[
19 @PREPARE_ENV@ 50 @PREPARE_ENV@
20 @PREPARE_INPUT_FILE@ 51 @PREPARE_INPUT_FILE@
21 #set $section = $sec_restrict 52 #set $section = $sec_restrict
22 @PREPARE_TARGETS_FILE@ 53 @PREPARE_TARGETS_FILE@
54 @PREPARE_REGIONS_FILE@
23 55
24 bcftools @EXECUTABLE@ 56 bcftools @EXECUTABLE@
25 57
26 #if $convert.convert_to == 'gen_sample': 58 #if $convert.convert_to == 'gen_sample':
27 --tag $convert.tag $convert.chrom $convert.vcf_ids 59 --tag $convert.tag $convert.chrom $convert.vcf_ids
31 --hapsample "$output_hap,$output_samples" 63 --hapsample "$output_hap,$output_samples"
32 #elif $convert.convert_to == 'hap_legend_sample': 64 #elif $convert.convert_to == 'hap_legend_sample':
33 $convert.vcf_ids $convert.haploid2diploid 65 $convert.vcf_ids $convert.haploid2diploid
34 --haplegendsample "$output_hap,$output_legend,$output_samples" 66 --haplegendsample "$output_hap,$output_legend,$output_samples"
35 #end if 67 #end if
68 @SAMPLE_SEX@
36 69
37 ## VCF input section 70 ## VCF input section
38 #set $section = $sec_restrict 71 #set $section = $sec_restrict
39 @INCLUDE@ 72 @INCLUDE@
40 @EXCLUDE@ 73 @EXCLUDE@
44 77
45 ## Primary Input/Outputs 78 ## Primary Input/Outputs
46 "$input_file" . 79 "$input_file" .
47 ]]> 80 ]]>
48 </command> 81 </command>
82 <configfiles>
83 <configfile name="entered_sex_file"><![CDATA[#slurp
84 #if $convert.sex_info.sex_info_src == 'entry':
85 $convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
86 #end if]]></configfile>
87 </configfiles>
49 <inputs> 88 <inputs>
50 <expand macro="macro_input" /> 89 <expand macro="macro_input" />
51 <section name="sec_restrict" expanded="false" title="Restrict to"> 90 <section name="sec_restrict" expanded="false" title="Restrict to">
52 <expand macro="macro_regions" /> 91 <expand macro="macro_regions" />
53 <expand macro="macro_targets" /> 92 <expand macro="macro_targets" />
71 --> 110 -->
72 </param> 111 </param>
73 <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false" 112 <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false"
74 label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/> 113 label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/>
75 <expand macro="macro_vcf_ids"/> 114 <expand macro="macro_vcf_ids"/>
115 <expand macro="macro_sexinfo"/>
76 </when> 116 </when>
77 <when value="hap_sample"> 117 <when value="hap_sample">
78 <expand macro="macro_haploid2diploid"/> 118 <expand macro="macro_haploid2diploid"/>
79 <expand macro="macro_vcf_ids"/> 119 <expand macro="macro_vcf_ids"/>
120 <expand macro="macro_sexinfo"/>
80 </when> 121 </when>
81 <when value="hap_legend_sample"> 122 <when value="hap_legend_sample">
82 <expand macro="macro_haploid2diploid"/> 123 <expand macro="macro_haploid2diploid"/>
83 <expand macro="macro_vcf_ids"/> 124 <expand macro="macro_vcf_ids"/>
125 <expand macro="macro_sexinfo"/>
84 </when> 126 </when>
85 </conditional> 127 </conditional>
86 </inputs> 128 </inputs>
87 <outputs> 129 <outputs>
88 <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen"> 130 <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">