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comparison complexity_bam.xml @ 8:9def47f3c1e4 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author nml
date Tue, 06 Aug 2019 08:50:28 -0400
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children 18aad692772a
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7:dcd43b402eb3 8:9def47f3c1e4
1 <tool id="complexity_bam" name="Complexity BAM" version="0.7.0">
2 <requirements>
3 <requirement type="package" version="0.7.0">quasitools</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6
7 ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' &&
8
9 quasitools complexity bam '$ref_file' '$input_bam' $k -f '$filter_size' -o output.csv
10
11 ]]></command>
12 <inputs>
13 <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" />
15 <param name="k" type="integer" label="k-mer size" value="0" min="0" />
16 <param name="filter_size" type="integer" label="Filter size" value="0" min="0" />
17 </inputs>
18 <outputs>
19 <data format="csv" name="output" from_work_dir="output.csv" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="ref_file" value="generated.fasta" />
24 <param name="input_bam" value="generated.bam" />
25 <param name="k" value="200" />
26 <param name="filter_size" value="0" />
27 <output name="output" >
28 <assert_contents>
29 <has_text text="Position" />
30 <has_text text="0" />
31 </assert_contents>
32 </output>
33 </test>
34 </tests>
35
36 <help><![CDATA[
37 Quasispecies Complexity
38 =======================
39
40 Calculates various quasispecies complexity measures on next generation sequenced data from a BAM file and it's corresponding reference file.
41
42 The measures of complexity are taken from the following work:
43 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
44
45
46 ]]></help>
47 <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>