Mercurial > repos > nml > quasitools

annotate complexity_fasta.xml @ 0:1f1214983a1c draft default tip

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 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:05:57 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
1 <tool id="complexity_fasta" name="Complexity FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
2 <macros>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
3 <import>macros.xml</import>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
4 </macros>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
5 <expand macro="requirements"/>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
7
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
8 quasitools complexity fasta '$input_fasta' -o output.csv
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
9
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
10 ]]></command>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
11 <inputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
12 <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
13 </inputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
14 <outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
15 <data format="csv" name="output" from_work_dir="output.csv" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
16 </outputs>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
17 <tests>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
18 <test>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
19 <param name="input_fasta" value="msa.fasta" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
20 <output name="output">
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
21 <assert_contents>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
22 <has_text text="Number of Haplotypes" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
23 <has_text text="8" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
24 <has_text text="0.75" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
25 </assert_contents>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
26 </output>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
27 </test>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
28 </tests>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
29
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
30 <help><![CDATA[
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
31 Quasispecies Complexity
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
32 =======================
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
33
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
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.
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
35
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
36 The measures of complexity are taken from the following work:
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
37
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
38 Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
39
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
40
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
41 ]]></help>
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
42 <expand macro="citations" />
1f1214983a1c planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
nml
parents:
diff changeset
43 </tool>