--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phmmer.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,85 @@
+<?xml version="1.0"?>
+<tool id="hmmer_phmmer" name="phmmer" version="@WRAPPER_VERSION@.0">
+  <description>search a protein sequence against a protein database (BLASTP-like)</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+phmmer
+
+@OFORMAT_WITH_OPTS@
+@HSSI@
+@THRESHOLDS@
+@ACCEL_HEUR@
+@EVAL_CALIB@
+@ADV_OPTS@
+
+@CPU@
+@SEED@
+
+$seqfile
+$seqdb
+> $output
+      ]]></command>
+  <inputs>
+    <param name="seqfile" type="data" format="fasta" label="Protein sequence to search with"/>
+    <!-- todo use Galaxy features like data libraries/data tables/??? -->
+    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
+    <expand macro="oformat_with_opts"/>
+    <expand macro="hssi"/>
+    <expand macro="thresholds_xml"/>
+    <expand macro="accel_heur_xml"/>
+    <expand macro="eval_calib_xml"/>
+    <expand macro="adv_opts"/>
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" label="PHMMER search of $seqfile.name in $seqdb.name"/>
+    <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $seqdb.name">
+      <filter>'tblout' in str(oformat)</filter>
+    </data>
+    <data format="txt" name="domtblout" label="Table of per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
+      <filter>'domtblout' in str(oformat)</filter>
+    </data>
+    <data format="txt" name="pfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $seqdb.name">
+      <filter>'pfamtblout' in str(oformat)</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="seqfile" value="globins45.fa"/>
+      <param name="seqdb" value="uniprot_matches.fasta"/>
+      <expand macro="oformat_test" />
+      <expand macro="seed_test" />
+      <output name="output" file="phmmer.out" lines_diff="200"/>
+      <!-- Lines diff is high due to a line of cpu/timing information for EACH sequence -->
+      <output name="domtblout" file="phmmer.domtblout" lines_diff="10"/>
+      <output name="pfamtblout" file="phmmer.pfamtblout" lines_diff="10"/>
+      <output name="tblout" file="phmmer.tblout" lines_diff="10"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+phmmer is used to search one or more query protein sequences against a protein
+sequence database.  For each query sequence in <seqfile>, use that sequence to
+search the target database of sequences in <seqdb>, and output ranked lists of
+the sequences with the most significant matches to the query.
+
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP@
+@HSSI_HELP@
+@THRESHOLDS_HELP@
+@ACCEL_HEUR_HELP@
+@EVAL_CALIB_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>