Mercurial > repos > iuc > sarscov2summary

annotate sarscov2summary.xml @ 0:4ad8b610ea41 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/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author iuc
date Mon, 04 May 2020 05:42:35 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
1 <tool id="sarscov2summary" name="sarscov2summary" version="0.1" profile="18.01">
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
2 <requirements>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
3 <requirement type="package" version="0.5">sarscov2summary</requirement>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
4 </requirements>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
5 <command><![CDATA[
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
6 sarscov2summary
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
7 -s '$slac'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
8 -f '$fel'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
9 -m '$meme'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
10 -p '$prime'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
11 -P $pvalue
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
12 -c '$coords'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
13 -D '$db'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
14 -d '$dups'
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
15 ]]></command>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
16 <inputs>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
17 <param name ="slac" type="data" format="json" label="HyPhy SLAC Output" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
18 <param name ="fel" type="data" format="json" label="HyPhy FEL Output" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
19 <param name ="meme" type="data" format="json" label="HyPhy MEME Output" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
20 <param name ="prime" type="data" format="json" label="HyPhy PRIME Output" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
21 <param name="pvalue" type="float" value="0.1" label="P-value" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
22 <param name="coords" type="data" format="fasta" label="Alignment With Reference" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
23 <param name="db" type="data" format="json" label="Metadata" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
24 <param name="dups" type="data" format="json" label="Duplicates" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
25 </inputs>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
26 <outputs>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
27 <data name="summary" format="json" from_work_dir="summary.json" label="Summary" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
28 </outputs>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
29 <tests>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
30 <test>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
31 <param name="slac" ftype="json" value="slac.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
32 <param name="fel" ftype="json" value="fel.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
33 <param name="meme" ftype="json" value="meme.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
34 <param name="prime" ftype="json" value="prime.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
35 <param name="coords" ftype="fasta" value="align.fasta" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
36 <param name="db" ftype="json" value="meta.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
37 <param name="dups" ftype="json" value="dups.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
38 <output name="summary" ftype="json" compare="diff" value="summary.json" />
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
39 </test>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
40 </tests>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
41 <help><![CDATA[
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
42 ===============
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
43 sarscov2summary
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
44 ===============
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
45
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
46 Custom summary script for the SARS-CoV2 Selection Analysis workflow. Takes HyPhy outputs as well as metadata to create final summary output.
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
47
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
48
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
49 ]]></help>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
50 <citations>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
51 <citation type="bibtex">
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
52 @misc{githubsarscov2summary,
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
53 author = {Sergei Pond},
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
54 year = {2020},
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
55 title = {sarscov2summary},
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
56 publisher = {Github},
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
57 journal = {Github repository},
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
58 url = {https://github.com/nickeener/sarscov2summary},
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
59 }</citation>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
60 </citations>
4ad8b610ea41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
iuc
parents:
diff changeset
61 </tool>