--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_to_trans_map.xml	Mon Aug 01 14:44:28 2016 -0400
@@ -0,0 +1,32 @@
+<tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@.0">
+    <description>for Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+       get_Trinity_gene_to_trans_map.pl "$assembly" > "$map"
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="map" label="${tool.name} on ${on_string}: Genes to transcripts map"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
+            <output name="map" file="raw/map.tsv" />
+        </test>
+    </tests>
+    <help>
+        Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+        This tool produces a file containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity.
+        The output file is intended to be used by the "Align reads and estimate abundance" tool.
+
+        .. _Trinity: http://trinityrnaseq.github.io
+    </help>
+
+    <expand macro="citation" />
+</tool>