--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mannwhitney_de.xml	Mon Jun 24 13:39:39 2019 -0400
@@ -0,0 +1,127 @@
+<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.0">
+    <description>using a Mann-Whitney test</description>
+    <requirements>
+        <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[ 
+        Rscript $__tool_directory__/MannWhitney_DE.R 
+            --input '$input' 
+            --sep 
+            #if $sep == 'tab':
+              'tab'
+            #elif $sep == 'comma':
+              'comma'
+            #end if
+            --colnames '$colnames'
+            --factor1 '$factor1'
+            --factor2 '$factor2'
+            --comparison_factor_file '$comparison_factor_file'
+            --fdr '$fdr'
+            $log
+            --output '$output'
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="txt,tabular" label="Expression data" help="a csv or tsv table file" />
+        <param name="sep" type="select" label="Indicate column separator">
+            <option value="tab" selected="true">Tabs</option>
+            <option value="comma">Comma</option>
+        </param>
+        <param name="colnames" type="select" label="Firt row contains column names">
+            <option value="TRUE" selected="true">Yes</option>
+            <option value="FALSE">No</option>
+        </param>
+        <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table"
+               help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories." />
+        <param name="factor1" type="text" label="Condition-1. The first level (value) that the comparison factor can take." help="typical values could be 'LOW', 'wt', 't1', etc."/>
+        <param name="factor2" type="text" label="Condition-2. The second level (value) that the comparison factor can take." help="typical values could be 'HIGH', 'mutant', 't2', etc."/>
+        <param name="fdr" type="float" value="0.01" label="FDR threshold"
+               help="Reject H0 of no differential expression if adjusted p-values (Benjamini-Hochberg correction) is higher than the FDR cut-off."/>
+        <param name="log" type="boolean" checked="false" label="Expression data are log-transformed" truevalue="--log" falsevalue=""/>
+
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="Results of Mann-Whitney differential analysis from ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="filtered-0.05.tab" ftype="txt"/>
+            <param name="sep" value="tab" />
+            <param name="colnames" value="TRUE"/>
+            <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/>
+            <param name="factor1" value="LOW"/>
+            <param name="factor2" value="HIGH"/>
+            <param name="fdr" value="0.01"/>
+            <param name="log" value="true"/>
+            <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="filterCells_100.tsv" ftype="txt"/>
+            <param name="sep" value="tab" />
+            <param name="colnames" value="TRUE"/>
+            <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/>
+            <param name="factor1" value="LOW"/>
+            <param name="factor2" value="HIGH"/>
+            <param name="fdr" value="0.01"/>
+            <param name="log" value="false"/>
+            <output name="output" file="geneMetadata_nolog.tsv" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+The tools takes a table of gene expression values (e.E. log2(CPM+1), etc...) from single cell RNAseq sequencing libraries (columns)
+
+and a metadata file that contains at least two columns :
+    * Cell identifiers
+    * A Column that differentiates cell in two groups (the two levels of a comparison factor). It must be a column with only values (the factor levels).
+
+For each gene (rows in expression data file), this script perform a 2-sided Mann-Whitney test between 
+the two groups of cells (high/low, mutant/wild type) and then adjust the returned p-values by using the
+Benjamini-Hochberg (BH) correction. A False Discovery Rate (FDR) threshold is used to determine if gene expression
+can be considered as significantly deviant for the H0 hypothesis of no-differential-expression (p-adjust below FDR cut-off) or not (p-adjust above the FDR cut-off). 
+
+.. class:: warningmark
+
+**Comparison plan**
+
+Note that log2Fold-Changes computed by the tool are based on the comparison of condition-2 (level-2) versus condition-1 (level-1) i.e.
+the tools returns the log2FC in condition-2 **relative** to condition-1.
+
+**Output**
+
+The tools returns a result table. For each row (genes) :
+
+==================== ======================================================================================================
+              Column Description
+-------------------- ------------------------------------------------------------------------------------------------------
+                mean mean expression across all cells
+                  SD standard deviation of its expression across all cells
+            variance variance of expression across all cells
+Percentage_detection (number of cells where the gene is detected (expression value superior to 0) / number of cells) * 100
+        mean_factor2 mean expression across cells of the second group (of log transformed expression values)
+        mean_factor1 mean expression across cells of the first group (of log transformed expression values)
+         fold_change mean_factor1 - mean_factor2 (difference of log)
+           statistic W statistic of Mann-Whitney test
+             p.value p-value of Mann-Whitney test
+            p.adjust p-values adjusted from the BH correction
+         Significant TRUE/FALSE vector (if p-adjust inferior to FDR cut-off then the value is TRUE) 
+==================== ======================================================================================================
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+        @Manual{,
+             title = {R: A Language and Environment for Statistical Computing},
+             author = {{R Core Team}},
+             organization = {R Foundation for Statistical Computing},
+             address = {Vienna, Austria},
+             year = {2014},
+             url = {http://www.R-project.org/},
+        }
+        </citation>
+    </citations>
+</tool>