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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
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="aacoverage" name="Amino Acid Coverage" version="0.7.0"> 1 <tool id="aacoverage" name="Amino Acid Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Builds an aa census and returns its coverage</description> 2 <description>Builds an aa census and returns its coverage</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}' &&
10 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
9 11
10 quasitools aacoverage $input_bam $ref_file $input_genes -o output.csv 12 quasitools aacoverage '${input_bam.name}' $ref_file $input_genes -o output.csv
11 13
12 ]]></command> 14 ]]></command>
13 <inputs> 15 <inputs>
14 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> 16 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
15 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> 17 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
42 **Output** 44 **Output**
43 45
44 A file with one entry per line with the AA position and the coverage at the position. 46 A file with one entry per line with the AA position and the coverage at the position.
45 47
46 ]]></help> 48 ]]></help>
47 <citations> 49 <expand macro="citations" />
48 <citation type="bibtex">
49 @misc{GitHubquasitoolsaacoverage,
50 title = {quasitools aacoverage},
51 publisher = {phac-nml},
52 journal = {GitHub repository},
53 url = {https://github.com/phac-nml/quasitools},
54 }
55 </citation>
56 </citations>
57 </tool> 50 </tool>