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comparison complexity_bam.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
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="complexity_bam" name="Complexity BAM" version="0.7.0"> 1 <tool id="complexity_bam" name="Complexity BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <requirements> 2 <macros>
3 <requirement type="package" version="0.7.0">quasitools</requirement> 3 <import>macros.xml</import>
4 </requirements> 4 </macros>
5 <expand macro="requirements"/>
5 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
6 7
7 ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' && 8 ln -s $input_bam '${input_bam.name}' &&
9 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
8 10
9 quasitools complexity bam '$ref_file' '$input_bam' $k -f '$filter_size' -o output.csv 11 quasitools complexity bam '$ref_file' '${input_bam.name}' $k -f '$filter_size' -o output.csv
10 12
11 ]]></command> 13 ]]></command>
12 <inputs> 14 <inputs>
13 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> 15 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
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" />
42 The measures of complexity are taken from the following work: 44 The measures of complexity are taken from the following work:
43 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237. 45 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
44 46
45 47
46 ]]></help> 48 ]]></help>
47 <citations> 49 <expand macro="citations" />
48 <citation type="bibtex">
49 @misc{GitHubquasitoolscomplexity,
50 title = {quasitools complexity},
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>