Mercurial > repos > nml > quasitools

comparison complexity_fasta.xml @ 8:9def47f3c1e4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author nml
date Tue, 06 Aug 2019 08:50:28 -0400
parents
children 18aad692772a
comparison
equal deleted inserted replaced
7:dcd43b402eb3 8:9def47f3c1e4
1 <tool id="complexity_fasta" name="Complexity FASTA" 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 quasitools complexity fasta '$input_fasta' -o output.csv
8
9 ]]></command>
10 <inputs>
11 <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" />
12 </inputs>
13 <outputs>
14 <data format="csv" name="output" from_work_dir="output.csv" />
15 </outputs>
16 <tests>
17 <test>
18 <param name="input_fasta" value="msa.fasta" />
19 <output name="output">
20 <assert_contents>
21 <has_text text="Number of Haplotypes" />
22 <has_text text="8" />
23 <has_text text="0.75" />
24 </assert_contents>
25 </output>
26 </test>
27 </tests>
28
29 <help><![CDATA[
30 Quasispecies Complexity
31 =======================
32
33 Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity.
34
35 The measures of complexity are taken from the following work:
36
37 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
38
39
40 ]]></help>
41 <citations>
42 <citation type="bibtex">
43 @misc{GitHubquasitoolscomplexity,
44 title = {quasitools complexity},
45 publisher = {phac-nml},
46 journal = {GitHub repository},
47 url = {https://github.com/phac-nml/quasitools},
48 }
49 </citation>
50 </citations>
51 </tool>