--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctat_edger_differential_expression.xml	Tue Jul 17 11:52:09 2018 -0400
@@ -0,0 +1,76 @@
+<tool id="ctat_edger_differential_expression" name="ctat_edger_differential_expression" version="1.0.0" profile="17.05">
+
+    <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
+    <requirements>
+        <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package">subprocess32</requirement>
+        <requirement type="package">bzip2</requirement>
+        <requirement type="package" version="1.3.0">rsem</requirement>
+        <requirement type="package" version="3">bioconductor-edger</requirement>
+        <requirement type="package" version="2">bioconductor-qvalue</requirement>
+        <requirement type="package" version="2.6.6">trinity</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+ 		python $__tool_directory__/ctat_edger_differential_expression.py 
+			$counts_matrix 
+			$dispersion
+        ]]>
+    </command>
+    <inputs>
+		
+		<param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
+		<param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
+		<param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
+	
+    </inputs>
+    <outputs>
+        <!--
+        <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
+       -->
+        <data format="txt" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
+			
+    </outputs>
+    <tests>
+	<test>
+	    <param name="counts_matrix" value="Sp.counts.matrix" />
+            <!-- The transcripts_fasta_file does not seem to be used for anything. -->
+	    <param name="transcripts_fasta_file" value="Sp.Trinity.fasta" />
+	    <param name="dispersion" value="0.1" />
+
+            <!-- One could create more detailed tests if the output files were explicitly
+                 saved rather than placed into an archive. We had a case where the archive
+                 was being created, but it was missing one of the files, or one of the
+                 files was empty. There is no easy way to look into the archive file to
+                 test this.
+            -->
+	    <output name="EdgeR_Archive" >
+                <assert_contents>
+                    <has_line_matching expression=".+" />
+                    <!-- The following is the magic number for all gzip files. -->
+                    <has_text_matching expression="\x1F\x8B" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+.. class:: infomark
+
+edgeR is a Bioconductor package focusing on the analysis of digital gene expression data derived from RNA-Seq sequencing technologies.
+
+To learn more about edgeR read their paper_, visit their website_ , or read this user_ guide_ .
+If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ .
+
+.. _paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/
+.. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
+.. _user: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
+.. _guide: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
+.. _website: http://bioinf.wehi.edu.au/edgeR/
+.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
+    </help>
+
+    <citations>
+        <citation type="doi">10.1038/nbt.1883</citation>
+    </citations>
+
+</tool>