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<tool id="experimentaldesign_igg" name="ExperimentalDesign" version="1.0">
	<description> </description>
	<command interpreter="bash">
		experimental_design/experimental_design.sh 
		#for $i, $f in enumerate($patients)
            "$f.id"
            #for $j, $g in enumerate($f.samples)
            	${g.sample}
            #end for
		#end for
		$out_file
	</command>
	<inputs>
		<repeat name="patients" title="Patient" min="1" default="1">
            <repeat name="samples" title="Sample" min="1" default="1">
                <param name="sample" format="tabular" type="data" label="Sample to Process" />
            </repeat>
			<param name="id" type="text" label="ID" />
		</repeat>
	</inputs>
	<outputs>
		<data format="tabular" name="out_file"/>
	</outputs>
	<help>
Takes the ARGalaxy proprietary format and merges several samples and/or patients together.
	</help>
 <citations>
    <!-- Example of annotating a citation using a DOI. -->
    <citation type="doi">10.1093/bioinformatics/btq281</citation>

    <!-- Example of annotating a citation using a BibTex entry. -->
    <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
    author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
    title = {An interior-point method for large-scale l1-regularized logistic regression},
    journal = {Journal of Machine Learning Research},
    year = {2007},
    volume = {8},
    pages = {1519-1555}
    }</citation>
  </citations>
  <tests>
    <test>
      <param name="input" value="1.bed"/>
      <param name="column" value="1"/>
      <param name="order" value="ASC"/>
      <param name="style" value="num"/>
      <output name="out_file1" file="sort1_num.bed"/>
    </test>
    <test>
      <param name="input" value="7.bed"/>
      <param name="column" value="1"/>
      <param name="order" value="ASC"/>
      <param name="style" value="alpha"/>
      <output name="out_file1" file="sort1_alpha.bed"/>
    </test>
  </tests>
</tool>