view abundance_estimates_to_matrix.xml @ 0:cc71440b759f draft default tip

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<tool id='abundance_estimates_to_matrix' name='abundance estimates to matrix' version='1.0'>
<description> Generates combined Matrix for abundance estimates </description>
<!--requirement></requirement-->
<requirements>
        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="R-module">edgeR</requirement>
        <requirement type="set_environment">TRINITY_HOME</requirement>

</requirements>
<command interpreter='perl'>\$TRINITY_HOME/util/abundance_estimates_to_matrix.pl 	
	--est_method $est_method  
	#for $i in $isoform_sample:
		$i.isoform_sample_matrix
	#end for
	&gt; $output_log 2&gt;&amp;1;
</command>

<inputs>
 <!-- Required -->

  <param name='est_method' type='select' display="radio"  label='Select est_method'>
  	<option value="RSEM" selected='true'>RSEM</option>
  	<option value="eXpress">eXpress</option>
  </param>


  <repeat name="isoform_sample" title="Isoform Sample" min="2">
 	 <param name="isoform_sample_matrix" type="data" label="Isoform Sample Matrix"/>	
  </repeat>

 <!-- Optional -->

</inputs>
<outputs>
	<data name='matrix_count' format='tabular' label="${tool.name} on ${on_string}: matrix_count" from_work_dir="matrix.counts.matrix"/>
	<data name='matrix_fpkm' format='tabular' label="${tool.name} on ${on_string} : matrix_fpkm" from_work_dir="matrix.TMM.fpkm.matrix"/>
	<data name='output_log' format='txt' label="${tool.name} on ${on_string} : matrix_log"/>
</outputs>
</tool>