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comparison callaavar.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
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="aavariants" name="Amino Acid Variants" version="0.7.0"> 1 <tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Identifies amino acid mutations</description> 2 <description>Identifies amino acid mutations</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 call aavar $input_bam $ref_file $input_genes 10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
11
12 quasitools call aavar '${input_bam.name}' $ref_file $input_genes
10 13
11 #if $var_file: 14 #if $var_file:
12 $var_file 15 $var_file
13 #end if 16 #end if
14 17
67 Identifies amino acid mutations for a BAM file. 70 Identifies amino acid mutations for a BAM file.
68 71
69 72
70 73
71 ]]></help> 74 ]]></help>
72 <citations> 75 <expand macro="citations" />
73 <citation type="bibtex">
74 @misc{GitHubquasitoolscallaavar,
75 title = {quasitools callaavar},
76 publisher = {phac-nml},
77 journal = {GitHub repository},
78 url = {https://github.com/phac-nml/quasitools},
79 }
80 </citation>
81 </citations>
82 </tool> 76 </tool>