--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_DE_analysis.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,146 @@
+<tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1">
+    <description>using a Trinity assembly</description>
+    <requirements>
+        <requirement type="package" version="2.1.1">trinity</requirement>
+        <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
+        <requirement type="package" version="1.10.0">deseq2</requirement>
+        <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
+        <requirement type="package" version="3.12.0">edger</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
+        <requirement type="package" version="3.25.3">limma</requirement>
+        <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+        
+        ln -s "${matrix}" "input.matrix"
+        
+        &&
+        
+        run_DE_analysis.pl
+        
+        --matrix "input.matrix"
+
+        --samples_file "${samples}"
+        
+        --method ${method_choice.method}
+        
+        #if $method_choice.method == "edgeR":
+            --dispersion ${method_choice.edger_dispersion}
+        #end if
+        
+        #if $method_choice.method == "ROTS":
+            --ROTS_B ${method_choice.rots_b}
+            --ROTS_K ${method_choice.rots_k}
+        #end if
+        
+        --min_rowSum_counts ${additional_params.min_rowSum_counts}
+        
+        #if $additional_params.reference_sample:
+            --reference_sample ${additional_params.reference_sample}
+        #end if
+        
+        #if $additional_params.contrasts:
+            --contrasts ${additional_params.contrasts}
+        #end if
+        
+        --output results
+        
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
+        <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/>
+        
+        <conditional name="method_choice">
+            <param type="select" name="method" label="Differential analysis method">
+                <option value="edgeR">edgeR</option>
+                <option value="DESeq2">DESeq2</option>
+                <option value="voom">voom</option>
+                <option value="ROTS">ROTS</option>
+            </param>
+            <when value="edgeR">
+                <param name="edger_dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
+            </when>
+            <when value="ROTS">
+                <param name="rots_b" type="integer" value="500" label="number of bootstraps and permutation resampling" />
+                <param name="rots_k" type="integer" value="5000" label="largest top genes size" />
+            </when>
+            <when value="voom">
+            </when>
+            <when value="DESeq2">
+            </when>
+        </conditional>
+        
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
+            <param name="reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
+            <param format="tabular" name="contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results" ext="tabular" directory="results" visible="true" />
+        </collection>
+        <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" ext="pdf" directory="results" visible="true" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <param name="method" value="DESeq2"/>
+            <output_collection name="DE_results">
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
+            </output_collection>
+            <output_collection name="PDF_results">
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool performs differential expression analyses on a transcriptome assembled with Trinity.
+
+**Inputs**
+
+This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
+
+You must describe your samples and replicates with a tabular file looking like this:
+
+=========== ================
+ConditionA  CondA_replicate1
+----------- ----------------
+ConditionA  CondA_replicate2
+----------- ----------------
+ConditionB  CondB_replicate1
+----------- ----------------
+ConditionB  CondB_replicate2
+----------- ----------------
+ConditionC  CondC_replicate1
+----------- ----------------
+ConditionC  CondC_replicate2
+----------- ----------------
+ConditionC  CondC_replicate3
+=========== ================
+
+It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
+The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+