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