<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>