# HG changeset patch
# User gkumar09
# Date 1443036266 14400
# Node ID 8bf618c08b4dfe46b498df264afc735787067374
# Parent  895cbd4424a502d82ffb264a6299c958a80d1f1a
Uploaded

diff -r 895cbd4424a5 -r 8bf618c08b4d RSEM_estimates_to_matrix.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RSEM_estimates_to_matrix.xml	Wed Sep 23 15:24:26 2015 -0400
@@ -0,0 +1,51 @@
+<tool id="RSEM_estimates_to_matrix" name="RSEM_estimates_to_matrix" version="0.0.1">
+
+    <description>Join RSEM estimates from multiple samples into a single matrix</description>
+    <requirements>
+        <requirement type="package">trinity</requirement>
+    </requirements>
+    <command interpreter="python">
+
+        trinityToolWrapper.py util/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
+
+		--labels
+        #for $entry in $RSEM_samples:
+        	${entry.column_label}
+        #end for
+
+		--RSEM_counts
+        #for $entry in $RSEM_samples:
+        	${entry.file}
+        #end for
+
+        > RSEM.counts.matrix
+
+    </command>
+    <inputs>
+
+       <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
+              <param name="file" label="Add file" type="data" format="text"/>
+              <param name="column_label" label="column label" type="text" />
+       </repeat>
+
+    </inputs>
+    <outputs>
+        <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.counts.matrix"/>
+	</outputs>
+    <tests>
+
+
+		<test>
+			<param name="target" value="trinity/Trinity.fasta" />
+			<param name="aligner" value="bowtie" />
+			<param name="paired_or_single" value="single" />
+			<param name="library_type" value="None" />
+			<param name="input" value="trinity/reads.left.fq" />
+        </test>
+	
+
+    </tests>
+    <help>
+        .. _Trinity: http://trinityrnaseq.sourceforge.net
+    </help>
+</tool>