Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison bcftools_convert_to_vcf.xml @ 7:367ba501b6eb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:05:01 -0500
parents 7b50ab23976c
children 843e008b15fd
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6:1f2183a23823 7:367ba501b6eb
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@VERSION@"> 2 <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@TOOL_VERSION@">
3 <description>Converts other formats to VCF/BCFk</description> 3 <description>Converts other formats to VCF/BCFk</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">convert</token> 5 <token name="@EXECUTABLE@">convert</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
68 <expand macro="macro_fasta_ref" /> 68 <expand macro="macro_fasta_ref" />
69 <expand macro="macro_samples"/> 69 <expand macro="macro_samples"/>
70 <expand macro="macro_columns"/> 70 <expand macro="macro_columns"/>
71 </when> 71 </when>
72 <when value="gvcf"> 72 <when value="gvcf">
73 <param name="input_file" type="data" format="gvcf" label="Genomic VCF (GATK HaplotypeCaller)" /> 73 <param name="input_file" type="data" format="vcf" label="Genomic VCF (GATK HaplotypeCaller)" />
74 <expand macro="macro_fasta_ref" /> 74 <expand macro="macro_fasta_ref" />
75 </when> 75 </when>
76 <when value="gen_sample"> 76 <when value="gen_sample">
77 <param name="input_file" type="data" format="tabular" label="The .gen file" /> 77 <param name="input_file" type="data" format="tabular" label="The .gen file" />
78 <param name="input_sample" type="data" format="tabular" label="The .samples file" /> 78 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
137 <param name="fasta_ref" ftype="fasta" value="gvcf.fa" /> 137 <param name="fasta_ref" ftype="fasta" value="gvcf.fa" />
138 <param name="output_type" value="v" /> 138 <param name="output_type" value="v" />
139 <output name="output_file"> 139 <output name="output_file">
140 <assert_contents> 140 <assert_contents>
141 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" /> 141 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
142 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tEND=20;BLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" /> 142 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
143 </assert_contents> 143 </assert_contents>
144 </output> 144 </output>
145 </test> 145 </test>
146 <test> 146 <test>
147 <param name="convert_from" value="tsv" /> 147 <param name="convert_from" value="tsv" />