Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff orthologs/hmmsearch.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/orthologs/hmmsearch.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,26 @@ +<tool id="phytab_hmmsearch" name="PHYTAB HMMSEARCH" version="3.0"> + <description>hmmsearch :: search profile(s) against a sequence database. Produces a phytab output.</description> + <requirements> + <requirement type="package">hmmsearch</requirement> + </requirements> + <command interpreter="python"> + hmmsearch.py -i $hmm -d $database > $hmmsearch_stdout 2>&1 + </command> + <inputs> + <param format="txt" name="hmm" type="data" label="HMM profiles" help="This should be a set of HMM models from hmmbuild"/> + <param format="txt" name="database" type="data" label="Sequence data" help="This should be a sequence database"/> + </inputs> + <outputs> + <data format="txt" name="hmmsearch_stdout" label="${tool.name} on ${on_string}: stdout" /> + <data format="txt" name="hmmsearch_results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" /> + </outputs> + <tests> + </tests> + <help> + **hmmsearch v3.0** + + Runs hmmsearch on HMM model data. + + See hmmsearch help: ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf + </help> +</tool>