Mercurial > repos > iuc > bcftools_gtcheck
comparison bcftools_gtcheck.xml @ 5:9d243d49870f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author | iuc |
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date | Thu, 13 Apr 2017 17:43:41 -0400 |
parents | d8c55ac67d89 |
children | a1213a0b7b66 |
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4:d8c55ac67d89 | 5:9d243d49870f |
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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[ |