--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/smrtpipe_hybrid.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,59 @@
+<tool id="smrtpipe_hybrid" name="AHA" version="1.0.0">
+  <description>Assemble contigs from a set of contigs and PacBio reads.</description>
+  <command interpreter="python">
+    smrtpipe_galaxy.py --nproc=24 --dat_extension=fasta --output=data/scaffold.fasta --galaxy_output=${outfile} ${iniFile}
+  </command>
+  <!--
+  <command>cp ${iniFile} ${outfile}</command>
+  -->
+  <inputs>
+    <param name="contigs" format="fasta" type="data" label="Starting Contigs"/>
+    <param name="reads" format="fasta" type="data" label="PacBio Reads"/>
+    <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/>
+  </inputs>
+  <configfiles>
+    <configfile name="iniFile">
+[input]
+assembled_contigs:${contigs}
+file:${reads}
+
+[HybridAssembly]
+instrumentModel=RS
+cleanup=False
+untangler=pacbio
+#set $schedule2 = $schedule.replace('X',';')
+paramSchedule=${schedule2}
+dontFillin=False
+longReadsAsStrobe=True
+exactQueryIds=True
+rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads
+numberProcesses=16
+cluster=False
+minRepeatLength=100000
+    </configfile>
+  </configfiles>
+  <outputs>
+    <data name="outfile" format="fasta" label="Hybrid assembly contigs from ${on_string}"/>
+  </outputs>
+  <help>
+
+**What it does**
+
+The AHA assembly algorithm is an AMOS_-based pipeline
+for finishing bacterial-sized
+genomes using draft contigs and PacBio reads.
+
+.. _AMOS: http://sourceforge.net/apps/mediawiki/amos
+
+**Parameter list**
+
+Parameter schedule
+    The parameter schedule is a semi-colon delimited list of triples.  Each triple represents an iteration of hybrid assembly (alignment/scaffolding/gap-filling).  The three paremeters for each iteration are the Z-score, number of reads required to define a link, and the minimum length of subreads used in links.
+
+**Output**
+
+FASTA file containing scaffolded and gap-filled contigs resulting from the 
+hybrid assembly.
+
+  </help>
+</tool>