diff abundance_estimates_to_matrix.xml @ 0:cc71440b759f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abundance_estimates_to_matrix.xml	Tue Sep 22 01:58:00 2015 -0400
@@ -0,0 +1,39 @@
+<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>