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diff orthologs/hmmsearch.xml @ 0:5b9a38ec4a39 draft default tip

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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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--- /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 > $hmmsearch_stdout 2>&amp;1
+  </command>
+  <inputs>
+    <param format="txt" name="hmm" type="data" label="HMM profiles" help="This should be a set of HMM models from hmmbuild"/>
+    <param format="txt" name="database" type="data" label="Sequence data" help="This should be a sequence database"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="hmmsearch_stdout" label="${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>