Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison bcftools_convert_to_vcf.xml @ 5:6911c0cb6b7d 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 16:21:34 -0400
parents dccf11c79157
children 45d35a05dbaa
comparison
equal deleted inserted replaced
4:dccf11c79157 5:6911c0cb6b7d
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>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <requirement type="package" version="1.3.1">samtools</requirement> 9 <expand macro="samtools_requirement"/>
10 </expand> 10 </expand>
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 13 @PREPARE_ENV@
14 #set $input_vcf = None 14 #set $input_vcf = None
15 #if $convert.convert_from == 'gvcf': 15 #if $convert.convert_from == 'gvcf':
16 #set $input_vcf = 'input.vcf.gz' 16 #set $input_vcf = 'input.vcf.gz'
17 #if $convert.input_file.is_of_type('vcf') 17 #if $convert.input_file.is_of_type('vcf')
18 bgzip -c "$convert.input_file" > $input_vcf && 18 bgzip -c '$convert.input_file' > $input_vcf &&
19 bcftools index $input_vcf && 19 bcftools index $input_vcf &&
20 #elif $convert.input_file.is_of_type('vcf_bgzip') 20 #elif $convert.input_file.is_of_type('vcf_bgzip')
21 ln -s "$convert.input_file" $input_vcf 21 ln -s '$convert.input_file' $input_vcf
22 #elif $convert.input_file.is_of_type('bcf') 22 #elif $convert.input_file.is_of_type('bcf')
23 #set $input_vcf = 'input.bcf' 23 #set $input_vcf = 'input.bcf'
24 ln -s "$convert.input_file" $input_vcf && 24 ln -s '$convert.input_file' $input_vcf &&
25 bcftools index $input_vcf && 25 bcftools index $input_vcf &&
26 #elif $convert.input_file.is_of_type('bcf_bgzip') 26 #elif $convert.input_file.is_of_type('bcf_bgzip')
27 ln -s "$convert.input_file" $input_vcf && 27 ln -s '$convert.input_file' $input_vcf &&
28 #end if 28 #end if
29 #end if 29 #end if
30 #set $section = $convert 30 #set $section = $convert
31 @PREPARE_FASTA_REF@ 31 @PREPARE_FASTA_REF@
32 32
34 34
35 @OUTPUT_TYPE@ 35 @OUTPUT_TYPE@
36 36
37 #set $section = $convert 37 #set $section = $convert
38 #if $convert.convert_from == 'gen_sample': 38 #if $convert.convert_from == 'gen_sample':
39 --gensample2vcf "$convert.input_file,$convert.input_sample" 39 --gensample2vcf '$convert.input_file,$convert.input_sample'
40 #elif $convert.convert_from == 'hap_sample': 40 #elif $convert.convert_from == 'hap_sample':
41 --hapsample2vcf "$convert.input_file,$convert.input_sample" 41 --hapsample2vcf '$convert.input_file,$convert.input_sample'
42 #elif $convert.convert_from == 'hap_legend_sample': 42 #elif $convert.convert_from == 'hap_legend_sample':
43 --haplegendsample2vcf "$convert.input_file,$convert.input_legend,$convert.input_sample" 43 --haplegendsample2vcf '$convert.input_file,$convert.input_legend,$convert.input_sample'
44 #elif $convert.convert_from == 'gvcf': 44 #elif $convert.convert_from == 'gvcf':
45 @FASTA_REF@ 45 @FASTA_REF@
46 --gvcf2vcf $input_vcf 46 --gvcf2vcf $input_vcf
47 #elif $convert.convert_from == 'tsv': 47 #elif $convert.convert_from == 'tsv':
48 @FASTA_REF@ 48 @FASTA_REF@
49 @SAMPLES@ 49 @SAMPLES@
50 @COLUMNS@ 50 @COLUMNS@
51 --tsv2vcf "$convert.input_file" 51 --tsv2vcf '$convert.input_file'
52 #end if 52 #end if
53 > "$output_file" 53 > '$output_file'
54 ]]> 54 ]]>
55 </command> 55 </command>
56 <inputs> 56 <inputs>
57 <conditional name="convert"> 57 <conditional name="convert">
58 <param name="convert_from" type="select" label="convert from"> 58 <param name="convert_from" type="select" label="convert from">