Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison bcftools_convert_to_vcf.xml @ 3:d6e3d97e17f0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Tue, 31 Jan 2017 12:42:27 -0500
parents b068ef999550
children 19167fd970a3
comparison
equal deleted inserted replaced
2:98d4a7bfec83 3:d6e3d97e17f0
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@ 11 @PREPARE_ENV@
12 #set $input_vcf = None 12 #set $input_vcf = None
13 #if $convert.convert_from == 'gvcf': 13 #if $convert.convert_from == 'gvcf':
14 #set $input_vcf = 'input.vcf.gz' 14 #set $input_vcf = 'input.vcf.gz'
15 #if $convert.input_file.datatype.file_ext == 'vcf' 15 #if $convert.input_file.is_of_type('vcf')
16 bgzip -c "$convert.input_file" > $input_vcf && 16 bgzip -c "$convert.input_file" > $input_vcf &&
17 bcftools index $input_vcf && 17 bcftools index $input_vcf &&
18 #elif $convert.input_file.datatype.file_ext == 'vcf_bgzip' 18 #elif $convert.input_file.is_of_type('vcf_bgzip')
19 ln -s "$convert.input_file" $input_vcf 19 ln -s "$convert.input_file" $input_vcf
20 #elif $convert.input_file.datatype.file_ext == 'bcf' 20 #elif $convert.input_file.is_of_type('bcf')
21 #set $input_vcf = 'input.bcf' 21 #set $input_vcf = 'input.bcf'
22 ln -s "$convert.input_file" $input_vcf && 22 ln -s "$convert.input_file" $input_vcf &&
23 bcftools index $input_vcf && 23 bcftools index $input_vcf &&
24 #elif $convert.input_file.datatype.file_ext == 'bcf_bgzip' 24 #elif $convert.input_file.is_of_type('bcf_bgzip')
25 ln -s "$convert.input_file" $input_vcf && 25 ln -s "$convert.input_file" $input_vcf &&
26 #end if 26 #end if
27 #end if 27 #end if
28 #set $section = $convert 28 #set $section = $convert
29 @PREPARE_FASTA_REF@ 29 @PREPARE_FASTA_REF@
59 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option> 59 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
60 <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option> 60 <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option>
61 <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option> 61 <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option>
62 </param> 62 </param>
63 <when value="tsv"> 63 <when value="tsv">
64 <param name="input_file" type="data" format="tabular" label="Tabular Variant Data" 64 <param name="input_file" type="data" format="tabular" label="Tabular Variant Data"
65 help="Reference sequence and samples are required"/> 65 help="Reference sequence and samples are required"/>
66 <expand macro="macro_fasta_ref" /> 66 <expand macro="macro_fasta_ref" />
67 <expand macro="macro_samples"/> 67 <expand macro="macro_samples"/>
68 <expand macro="macro_columns"/> 68 <expand macro="macro_columns"/>
69 </when> 69 </when>