--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jackhmmer.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,96 @@
+<?xml version="1.0"?>
+<tool id="hmmer_jackhmmer" name="jackhmmer" version="@WRAPPER_VERSION@.0">
+  <description>iteratively search a protein sequence against a protein database (PSIBLAST-like)</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+jackhmmer
+-N $N
+@OFORMAT_WITH_OPTS_NOPFAM@
+@HSSI@
+@THRESHOLDS@
+@ACCEL_HEUR@
+@MCSS@
+@ARSWS@
+@AEEWS@
+@PRIOR@
+
+@EVAL_CALIB@
+@ADV_OPTS@
+@CPU@
+@SEED@
+
+$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="N" type="integer" value="5" min="1" label="Maximum number of iterations" help="(-N)"/>
+    <param name="seqdb" type="data" format="fasta" label="Sequence Database"/>
+    <expand macro="oformat_with_opts_nopfam"/>
+    <expand macro="hssi"/>
+    <expand macro="thresholds_xml"/>
+    <expand macro="accel_heur_xml"/>
+    <expand macro="mcss"/>
+    <expand macro="arsws"/>
+    <expand macro="aeews"/>
+    <expand macro="prior"/>
+    <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>
+  </outputs>
+  <tests>
+    <test>
+      <param name="seqfile" value="uniprot_matches.fasta"/>
+      <param name="seqdb" value="globins45.fa"/>
+      <expand macro="oformat_test" />
+      <expand macro="seed_test" />
+      <output name="output" file="jackhmmer.out" lines_diff="180"/>
+      <output name="domtblout" file="jackhmmer.domtblout" lines_diff="10"/>
+      <output name="tblout" file="jackhmmer.tblout" lines_diff="10"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+jackhmmer iteratively searches each query sequence in <seqfile> against the
+target sequence(s) in <seqdb>. The first iteration is identical to a phmmer
+search. For the next iteration, a multiple alignment of the query together
+with all target sequences satisfying inclusion thresholds is assembled, a
+profile is constructed from this alignment (identical to using hmmbuild on the
+alignment), and profile search of the <seqdb> is done (identical to an
+hmmsearch with the profile).
+
+
+@HELP_PRE_OTH@
+
+@OFORMAT_WITH_OPTS_HELP_NOPFAM@
+@HSSI_HELP@
+@THRESHOLDS_HELP@
+@ACCEL_HEUR_HELP@
+@MCSS_HELP@
+@ARSWS_HELP@
+@AEEWS_HELP@
+@PRIOR_HELP@
+@EVAL_CALIB_HELP@
+@ADV_OPTS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>