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comparison drmutations.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
comparison
equal deleted inserted replaced
8:9def47f3c1e4 9:18aad692772a
1 <tool id="drmutations" name="Drug Resistance Mutations" version="0.7.0"> 1 <tool id="drmutations" name="Drug Resistance Mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description> 2 <description></description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.0">quasitools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 8
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 9 ln -s $input_bam '${input_bam.name}' &&
9 quasitools drmutations $input_bam $ref_file $var_file $input_genes 10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
11
12 quasitools drmutations '${input_bam.name}' $ref_file $var_file $input_genes
10 13
11 #if $mutation_db: 14 #if $mutation_db:
12 $mutation_db 15 $mutation_db
13 #end if 16 #end if
14 17
79 ------- 82 -------
80 83
81 A CSV file containing the drug resistant mutations found. 84 A CSV file containing the drug resistant mutations found.
82 85
83 ]]></help> 86 ]]></help>
84 <citations> 87 <expand macro="citations" />
85 <citation type="bibtex">
86 @misc{GitHubquasitoolsdrmutations,
87 title = {quasitools drmutations},
88 publisher = {phac-nml},
89 journal = {GitHub repository},
90 url = {https://github.com/phac-nml/quasitools},
91 }
92 </citation>
93 </citations>
94 </tool> 88 </tool>