Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison orthologs/hmmsearch.xml @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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-1:000000000000 | 0:5b9a38ec4a39 |
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1 <tool id="phytab_hmmsearch" name="PHYTAB HMMSEARCH" version="3.0"> | |
2 <description>hmmsearch :: search profile(s) against a sequence database. Produces a phytab output.</description> | |
3 <requirements> | |
4 <requirement type="package">hmmsearch</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 hmmsearch.py -i $hmm -d $database > $hmmsearch_stdout 2>&1 | |
8 </command> | |
9 <inputs> | |
10 <param format="txt" name="hmm" type="data" label="HMM profiles" help="This should be a set of HMM models from hmmbuild"/> | |
11 <param format="txt" name="database" type="data" label="Sequence data" help="This should be a sequence database"/> | |
12 </inputs> | |
13 <outputs> | |
14 <data format="txt" name="hmmsearch_stdout" label="${tool.name} on ${on_string}: stdout" /> | |
15 <data format="txt" name="hmmsearch_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" /> | |
16 </outputs> | |
17 <tests> | |
18 </tests> | |
19 <help> | |
20 **hmmsearch v3.0** | |
21 | |
22 Runs hmmsearch on HMM model data. | |
23 | |
24 See hmmsearch help: ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf | |
25 </help> | |
26 </tool> |