<tool id="cap3" name="cap3" version="2.0.1">
<description>Sequence Assembly tool</description>
    <requirements>
        <requirement type="package" version="10.2011=1">cap3</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
    cap3 "$inputSequences" -o $overlaplength -p $overlapidentity > "$cap3stdout" &&
                mv "$inputSequences".cap.contigs $contigs &&
                mv "$inputSequences".cap.contigs.qual $contigsqual &&
                mv "$inputSequences".cap.contigs.links $contigslink &&
                mv "$inputSequences".cap.ace $ace &&
                mv "$inputSequences".cap.info $info &&
                mv "$inputSequences".cap.singlets $singlets &&
                cat $contigs $singlets > $contigsandsinglets
    ]]></command>

        <inputs>
        	<param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
        	<param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" />
        	<param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90"  help="-p option. must be > 65. 90 by default" />
        </inputs>

<outputs>
                <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" />
        	    <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/>
                <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
                <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" />
                <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" />
                <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" />
                <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" />
                <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" />
</outputs>

  <tests>
    <test>
      <param name="inputSequences" value="input.fa" ftype="fasta"/>
      <param name="overlaplength" value="40" />
      <param name="overlapidentity" value="90" />
      <output name="contigsandsinglets" file="contigsandsinglets.fa"/>
      <output name="cap3stdout" file="cap3stdout.txt"/>
      <output name="contigs" file="contigs.fa"/>
      <output name="contigsqual" file="contigsqual.txt"/>
      <output name="contigslink" file="contigslink.txt"/>
      <output name="ace" file="ace.txt"/>
      <output name="info" file="info.txt"/>
      <output name="singlets" file="singlets.fa"/>
    </test>
  </tests>


<help>
**What it does**

This tool is a CAP3 wrapper developed for the visitor2 set of worflows

Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences

Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets).

Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets)

**Acknowledgments**

This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson.

It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.

.. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3
.. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
.. _MIT license: http://opensource.org/licenses/MIT


</help>
  <citations>
      <citation type="bibtex">@article{Huang:1999wb,
       author = {Huang, X and Madan, A},
       title = {{CAP3: A DNA sequence assembly program.}},
       journal = {Genome research},
       year = {1999},
       volume = {9},
       number = {9},
      pages = {868--877},
      month = sep
      }
      </citation>
  </citations>
  
</tool>