--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/super_transcripts.xml	Thu Jun 14 03:12:34 2018 -0400
@@ -0,0 +1,35 @@
+<tool id="trinity_super_transcripts" name="Generate SuperTranscripts" version="@WRAPPER_VERSION@">
+    <description>from a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+       Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta '$assembly'
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="seqs" from_work_dir="trinity_genes.fasta" label="${tool.name} on ${on_string}: SuperTranscripts sequences"/>
+        <data format="gtf" name="annotation" from_work_dir="trinity_genes.gtf" label="${tool.name} on ${on_string}: SuperTranscripts strcture annotation"/>
+        <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
+            <output name="seqs" file="supertranscripts/trinity_genes.fasta" />
+            <output name="annotation" file="supertranscripts/trinity_genes.gtf" />
+            <output name="malign" file="supertranscripts/trinity_genes.malign" />
+        </test>
+    </tests>
+    <help>
+        SuperTranscripts provide a gene-like view of the transcriptional complexity of a gene. SuperTranscripts were originally defined by Nadia Davidson, Anthony Hawkins, and Alicia Oshlack as described in their publication "SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes" Genome Biology, 2017. SuperTranscripts are useful in the context of genome-free de novo transcriptome assembly in that they provide a genome-like reference for studying aspects of the gene including differential transcript usage (aka. differential exon usage) and as a substrate for mapping reads and identifying allelic polymorphisms.
+
+        A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence.
+
+        .. _Trinity: http://trinityrnaseq.github.io
+    </help>
+
+    <expand macro="citation" />
+</tool>