Mercurial > repos > iuc > ivar_variants

comparison ivar_variants.xml @ 15:045d6d00f606 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
author iuc
date Tue, 27 Jun 2023 17:13:41 +0000
parents ed28dd32141c
children
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14:230b05597996 15:045d6d00f606
1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>Call variants from aligned BAM file</description> 2 <description>Call variants from aligned BAM file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}"> 57 <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter> 58 <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
59 </data> 59 </data>
60 </outputs> 60 </outputs>
61 <tests> 61 <tests>
62 <test expect_num_outputs="1"> 62 <test expect_num_outputs="1"> <!-- test 1 -->
63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> 63 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
64 <param name="ref" value="zika/db/PRV.fa"/> 64 <param name="ref" value="zika/db/PRV.fa"/>
65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/> 65 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/>
66 </test> 66 </test>
67 <test expect_num_outputs="1"> 67 <test expect_num_outputs="1"> <!-- test 2 -->
68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> 68 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
69 <param name="ref" value="zika/db/PRV.fa"/> 69 <param name="ref" value="zika/db/PRV.fa"/>
70 <conditional name="output_format"> 70 <conditional name="output_format">
71 <param name="choice" value="vcf"/> 71 <param name="choice" value="vcf"/>
72 </conditional> 72 </conditional>
73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/> 73 <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/>
74 </test> 74 </test>
75 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2"> <!-- test 3 -->
76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> 76 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
77 <param name="ref" value="zika/db/PRV.fa"/> 77 <param name="ref" value="zika/db/PRV.fa"/>
78 <conditional name="output_format"> 78 <conditional name="output_format">
79 <param name="choice" value="tabular_and_vcf"/> 79 <param name="choice" value="tabular_and_vcf"/>
80 <param name="pass_only" value="true"/> 80 <param name="pass_only" value="true"/>
81 </conditional> 81 </conditional>
82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/> 82 <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/>
83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/> 83 <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
84 </test> 84 </test>
85 <test expect_num_outputs="1"> 85 <test expect_num_outputs="1"> <!-- test 4 -->
86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> 86 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
87 <param name="ref" value="zika/db/PRV.fa"/> 87 <param name="ref" value="zika/db/PRV.fa"/>
88 <param name="gtf" value="zika/db/PRV.gff"/> 88 <param name="gtf" value="zika/db/PRV.gff"/>
89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/> 89 <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
90 </test> 90 </test>
91 <test expect_num_outputs="2"> 91 <test expect_num_outputs="2"> <!-- test 5 -->
92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/> 92 <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
93 <param name="ref" value="zika/db/PRV.fa"/> 93 <param name="ref" value="zika/db/PRV.fa"/>
94 <param name="gtf" value="zika/db/PRV.gff"/> 94 <param name="gtf" value="zika/db/PRV.gff"/>
95 <conditional name="output_format"> 95 <conditional name="output_format">
96 <param name="choice" value="tabular_and_vcf"/> 96 <param name="choice" value="tabular_and_vcf"/>