Mercurial > repos > iuc > sarscov2summary
comparison sarscov2summary.xml @ 0:4ad8b610ea41 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary commit a9dbee25f6ad053c0c9b78f85276c7c839d2ab7a"
author | iuc |
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date | Mon, 04 May 2020 05:42:35 -0400 |
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-1:000000000000 | 0:4ad8b610ea41 |
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1 <tool id="sarscov2summary" name="sarscov2summary" version="0.1" profile="18.01"> | |
2 <requirements> | |
3 <requirement type="package" version="0.5">sarscov2summary</requirement> | |
4 </requirements> | |
5 <command><![CDATA[ | |
6 sarscov2summary | |
7 -s '$slac' | |
8 -f '$fel' | |
9 -m '$meme' | |
10 -p '$prime' | |
11 -P $pvalue | |
12 -c '$coords' | |
13 -D '$db' | |
14 -d '$dups' | |
15 ]]></command> | |
16 <inputs> | |
17 <param name ="slac" type="data" format="json" label="HyPhy SLAC Output" /> | |
18 <param name ="fel" type="data" format="json" label="HyPhy FEL Output" /> | |
19 <param name ="meme" type="data" format="json" label="HyPhy MEME Output" /> | |
20 <param name ="prime" type="data" format="json" label="HyPhy PRIME Output" /> | |
21 <param name="pvalue" type="float" value="0.1" label="P-value" /> | |
22 <param name="coords" type="data" format="fasta" label="Alignment With Reference" /> | |
23 <param name="db" type="data" format="json" label="Metadata" /> | |
24 <param name="dups" type="data" format="json" label="Duplicates" /> | |
25 </inputs> | |
26 <outputs> | |
27 <data name="summary" format="json" from_work_dir="summary.json" label="Summary" /> | |
28 </outputs> | |
29 <tests> | |
30 <test> | |
31 <param name="slac" ftype="json" value="slac.json" /> | |
32 <param name="fel" ftype="json" value="fel.json" /> | |
33 <param name="meme" ftype="json" value="meme.json" /> | |
34 <param name="prime" ftype="json" value="prime.json" /> | |
35 <param name="coords" ftype="fasta" value="align.fasta" /> | |
36 <param name="db" ftype="json" value="meta.json" /> | |
37 <param name="dups" ftype="json" value="dups.json" /> | |
38 <output name="summary" ftype="json" compare="diff" value="summary.json" /> | |
39 </test> | |
40 </tests> | |
41 <help><![CDATA[ | |
42 =============== | |
43 sarscov2summary | |
44 =============== | |
45 | |
46 Custom summary script for the SARS-CoV2 Selection Analysis workflow. Takes HyPhy outputs as well as metadata to create final summary output. | |
47 | |
48 | |
49 ]]></help> | |
50 <citations> | |
51 <citation type="bibtex"> | |
52 @misc{githubsarscov2summary, | |
53 author = {Sergei Pond}, | |
54 year = {2020}, | |
55 title = {sarscov2summary}, | |
56 publisher = {Github}, | |
57 journal = {Github repository}, | |
58 url = {https://github.com/nickeener/sarscov2summary}, | |
59 }</citation> | |
60 </citations> | |
61 </tool> |