Mercurial > repos > nml > quasitools

annotate complexity.xml @ 7:dcd43b402eb3 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 ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author nml
date Fri, 23 Nov 2018 15:43:16 -0500
parents 9fb9fed71486
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
1 <tool id="complexity" name="Complexity" version="0.5.1">
6
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
2 <description>measures the complexity of the quasispecies reads</description>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
3 <requirements>
7
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
4 <requirement type="package" version="0.5.1">quasitools</requirement>
6
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
5 </requirements>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
7
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
8 quasitools complexity $input_fasta > complexity.txt
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
9
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
10 ]]></command>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
11 <inputs>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
12 <param name="input_fasta" type="data" format="fasta" optional="false" label="Aligned FASTA Input" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
13 </inputs>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
14 <outputs>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
15 <data format="txt" label="Complexity" name="output_complexity" from_work_dir="complexity.txt" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
16 </outputs>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
17
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
18 <tests>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
19 <test>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
20 <param name="input_fasta" value="msa.fasta" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
21 <output name="output_complexity">
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
22 <assert_contents>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
23 <has_text text="Number of haplotypes (H) : 8" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
24 <has_text text="Mutation Frequency (Mfe) : 0.75" />
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
25 </assert_contents>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
26 </output>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
27 </test>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
28 </tests>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
29
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
30 <help><![CDATA[
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
31 Quasispecies Complexity
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
32 =======================
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
33
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
34 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.
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
35
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
36 The measures of complexity are taken from the following work:
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
37
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
38 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
39
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
40
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
41 ]]></help>
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
42 <citations>
7
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
43 <citation type="bibtex">
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
44 @misc{GitHubquasitoolscomplexity,
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
45 title = {quasitools complexity},
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
46 publisher = {phac-nml},
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
47 journal = {GitHub repository},
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
48 url = {https://github.com/phac-nml/quasitools},
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
49 }
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
50 </citation>
dcd43b402eb3 planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
nml
parents: 6
diff changeset
51 </citations>
6
9fb9fed71486 planemo upload for repository https://github.com/phac-nml/quasitools commit 59e7cd4a6042f14a07488489a1dc3b05ee3bc15c
nml
parents:
diff changeset
52 </tool>