Mercurial > repos > iuc > bcftools_gtcheck

comparison bcftools_gtcheck.xml @ 5:9d243d49870f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:43:41 -0400
parents d8c55ac67d89
children a1213a0b7b66
comparison
equal deleted inserted replaced
4:d8c55ac67d89 5:9d243d49870f
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@ 11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@ 12 @PREPARE_INPUT_FILE@
13 #set $section = $sec_restrict 13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 14 @PREPARE_TARGETS_FILE@
15 @PREPARE_REGIONS_FILE@
15 #set $section = $sec_default 16 #set $section = $sec_default
16 #set $genotypes_vcf = None 17 #set $genotypes_vcf = None
17 #if $section.genotypes: 18 #if $section.genotypes:
18 #if $section.genotypes.is_of_type('vcf') 19 #if $section.genotypes.is_of_type('vcf')
19 #set $genotypes_vcf = 'genotypes.vcf.gz' 20 #set $genotypes_vcf = 'genotypes.vcf.gz'
20 bgzip -c "$section.genotypes" > $genotypes_vcf && 21 bgzip -c '$section.genotypes' > $genotypes_vcf &&
21 bcftools index $genotypes_vcf && 22 bcftools index $genotypes_vcf &&
22 #elif $section.genotypes.is_of_type('bcf') 23 #elif $section.genotypes.is_of_type('bcf')
23 #set $genotypes_vcf = 'genotypes.bcf' 24 #set $genotypes_vcf = 'genotypes.bcf'
24 ln -s "$ection.genotypes" $genotypes_vcf && 25 ln -s '$ection.genotypes' $genotypes_vcf &&
25 #if $section.genotypes.metadata.bcf_index: 26 #if $section.genotypes.metadata.bcf_index:
26 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi && 27 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
27 #else 28 #else
28 bcftools index $genotypes_vcf && 29 bcftools index $genotypes_vcf &&
29 #end if 30 #end if
38 #if $genotypes_vcf: 39 #if $genotypes_vcf:
39 --genotypes $genotypes_vcf 40 --genotypes $genotypes_vcf
40 #end if 41 #end if
41 42
42 #if $section.genotypes: 43 #if $section.genotypes:
43 --genotypes "${section.genotypes}" 44 --genotypes '${section.genotypes}'
44 #end if 45 #end if
45 46
46 ${section.all_sites} 47 ${section.all_sites}
47 48
48 #if $section.GTs_only: 49 #if $section.GTs_only:
49 --GTs-only "${section.GTs_only}" 50 --GTs-only '${section.GTs_only}'
50 #end if 51 #end if
51 52
52 ${section.homs_only} 53 ${section.homs_only}
53 54
54 #if $section.plot: 55 #if $section.plot:
55 --plot "${section.plot}" 56 --plot '${section.plot}'
56 #end if 57 #end if
57 58
58 #if $section.query_sample: 59 #if $section.query_sample:
59 --query-sample "${section.query_sample}" 60 --query-sample '${section.query_sample}'
60 #end if 61 #end if
61 62
62 #if $section.target_sample: 63 #if $section.target_sample:
63 --target-sample "${section.target_sample}" 64 --target-sample '${section.target_sample}'
64 #end if 65 #end if
65 66
66 #set $section = $sec_restrict 67 #set $section = $sec_restrict
67 @REGIONS@ 68 @REGIONS@
68 @TARGETS@ 69 @TARGETS@
69 70
70 ## Primary Input/Outputs 71 ## Primary Input/Outputs
71 72
72 @INPUT_FILE@ 73 @INPUT_FILE@
73 > "$output_file" 74 > '$output_file'
74 ]]> 75 ]]>
75 </command> 76 </command>
76 <inputs> 77 <inputs>
77 <expand macro="macro_input" /> 78 <expand macro="macro_input" />
78 <section name="sec_restrict" expanded="false" title="Restrict to"> 79 <section name="sec_restrict" expanded="false" title="Restrict to">
94 <data name="output_file" format="tabular" /> 95 <data name="output_file" format="tabular" />
95 </outputs> 96 </outputs>
96 <tests> 97 <tests>
97 <test> 98 <test>
98 <param name="input_file" ftype="vcf" value="view.vcf" /> 99 <param name="input_file" ftype="vcf" value="view.vcf" />
99 <param name="GTs_only" value="" /> 100 <param name="GTs_only" value="99" />
100 <output name="output_file"> 101 <output name="output_file">
101 <assert_contents> 102 <assert_contents>
102 <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/> 103 <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/>
103 <has_text_matching expression="CN\t1174\t14\t75.57\tNA00002\tNA00001"/>
104 </assert_contents> 104 </assert_contents>
105 </output> 105 </output>
106 </test> 106 </test>
107 </tests> 107 </tests>
108 <help><![CDATA[ 108 <help><![CDATA[