Mercurial > repos > iuc > vsnp_add_zero_coverage

comparison vsnp_add_zero_coverage.xml @ 6:12b6574f1db0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
author iuc
date Tue, 16 Nov 2021 20:05:31 +0000
parents de548dd07fd3
children 7fe5d7ddf81b
comparison
equal deleted inserted replaced
5:de548dd07fd3 6:12b6574f1db0
1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@WRAPPER_VERSION@.2+galaxy0" profile="@PROFILE@"> 1 <tool id="vsnp_add_zero_coverage" name="vSNP: add zero coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.0.7">openpyxl</requirement> 7 <expand macro="biopython_requirement"/>
8 <requirement type="package" version="1.79">biopython</requirement> 8 <expand macro="openpyxl_requirement"/>
9 <requirement type="package" version="1.3.0">pandas</requirement> 9 <expand macro="pandas_requirement"/>
10 <requirement type="package" version="0.16.0.1">pysam</requirement> 10 <requirement type="package" version="0.16.0.1">pysam</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #import re 13 #import re
14 14
56 <test expect_num_outputs="2"> 56 <test expect_num_outputs="2">
57 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> 57 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
58 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> 58 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
59 <param name="reference_source" value="history"/> 59 <param name="reference_source" value="history"/>
60 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/> 60 <param name="reference" value="NC_002945v4.fasta" ftype="fasta"/>
61 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/> 61 <output name="output_vcf" ftype="vcf">
62 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular"/> 62 <assert_contents>
63 <has_size value="259726"/>
64 </assert_contents>
65 </output>
66 <output name="output_metrics" ftype="tabular">
67 <assert_contents>
68 <has_size value="109"/>
69 </assert_contents>
70 </output>
63 </test> 71 </test>
64 <test expect_num_outputs="2"> 72 <test expect_num_outputs="2">
65 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/> 73 <param name="bam_input" value="bam_input.bam" ftype="bam" dbkey="89"/>
66 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/> 74 <param name="vcf_input" value="vcf_input.vcf" ftype="vcf" dbkey="89"/>
67 <param name="reference_source" value="cached"/> 75 <param name="reference_source" value="cached"/>
68 <output name="output_vcf" value="output_vcf.vcf" ftype="vcf" compare="contains"/> 76 <output name="output_vcf" ftype="vcf">
69 <output name="output_metrics" file="output_metrics.tabular" ftype="tabular" compare="contains"/> 77 <assert_contents>
78 <has_size value="259726"/>
79 </assert_contents>
80 </output>
81 <output name="output_metrics" ftype="tabular">
82 <assert_contents>
83 <has_size value="109"/>
84 </assert_contents>
85 </output>
70 </test> 86 </test>
71 </tests> 87 </tests>
72 <help> 88 <help>
73 **What it does** 89 **What it does**
74 90
81 97
82 **Required Options** 98 **Required Options**
83 99
84 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history. 100 * **Choose the source for the reference genome** - select "locally cached" if the reference associated with the BAM and VCF files is available within the Galaxy environment or "from history" to select the reference from the current history.
85 </help> 101 </help>
86 <expand macro="citations" /> 102 <expand macro="citations"/>
87 </tool> 103 </tool>
88 104