--- a/limma_voom.xml	Sun May 05 09:02:04 2019 -0400
+++ b/limma_voom.xml	Tue May 28 10:04:10 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="limma_voom" name="limma" version="3.38.3+galaxy2">
+<tool id="limma_voom" name="limma" version="3.38.3+galaxy3">
     <description>
         Perform differential expression with limma-voom or limma-trend
     </description>
@@ -57,7 +57,11 @@
     -a '$anno.geneanno'
 #end if
 
--C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
+#if $cont.cfile=='yes':
+    -C '$cont.cinfo'
+#else: 
+    -D '${ ','.join( ['%s' % $x.contrast for x in $cont.rep_contrast] ) }'
+#end if
 
 #if $f.filt.filt_select == 'yes':
     #if $f.filt.cformat.format_select == 'cpm':
@@ -223,12 +227,24 @@
         </conditional>
 
         <!-- Contrasts -->
-        <repeat name="rep_contrast" title="Contrast" min="1" default="1">
-            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
-                <validator type="empty_field" />
-                <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
+        <conditional name="cont">
+            <param name="cfile" type="select" label="Input Contrast information from file?"
+                help="You can choose to input the contrast information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), the group names MUST not contain hyphens. Use a hyphen to separate the groups you want to compare, as shown in the Help section below.">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
             </param>
-        </repeat>
+            <when value="yes">
+                <param name="cinfo" type="data" format="tabular" label="Contrasts File"/>
+            </when>
+            <when value="no" >
+                <repeat name="rep_contrast" title="Contrast" min="1" default="1">
+                    <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (Mut1-Ctrl1)-(Mut2-Ctrl2). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
+                    <validator type="empty_field" />
+                    <validator type="regex" message="Please only use letters, numbers or underscores">^[\(\w\)-]+$</validator>
+                    </param> 
+                </repeat>
+            </when>
+        </conditional>
 
         <!-- Filter Options -->
         <section name="f" expanded="false" title="Filter Low Counts">
@@ -360,6 +376,7 @@
                 <param name="factorName" value="Genotype"/>
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -400,6 +417,7 @@
                 <param name="factorName" value="Genotype"/>
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -424,6 +442,7 @@
                 <param name="factorName" value="Genotype"/>
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -452,6 +471,7 @@
                 <param name="factorName" value="Batch"/>
                 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -472,6 +492,7 @@
             <param name="ffile" value="yes" />
             <param name="finfo" value="factorinfo.txt" />
             <param name="counts" value="matrix.txt" />
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -496,6 +517,7 @@
                 <param name="factorName" value="Genotype"/>
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -559,6 +581,7 @@
             </repeat>
             <param name="annoOpt" value="yes" />
             <param name="geneanno" value="anno.txt" />
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -596,6 +619,7 @@
                 <param name="factorName" value="Genotype"/>
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -626,6 +650,7 @@
                 <param name="factorName" value="Genotype"/>
                 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="Mut-WT" />
             </repeat>
@@ -656,6 +681,7 @@
                 <param name="factorName" value="Group"/>
                 <param name="groupNames" value="2,2,2,1,1,1" />
             </repeat>
+            <param name="cfile" value="no" />
             <repeat name="rep_contrast">
                 <param name="contrast" value="2-1" />
             </repeat>
@@ -683,6 +709,33 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Ensure contrasts file works -->
+        <test expect_num_outputs="2">
+            <param name="format" value="matrix" />
+            <param name="counts" value="matrix.txt" />
+            <repeat name="rep_factor">
+                <param name="factorName" value="Genotype"/>
+                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
+            </repeat>
+            <param name="cfile" value="yes" />
+            <param name="cinfo" value="contrasts.txt" />
+            <param name="normalisationOption" value="TMM" />
+            <param name="topgenes" value="6" />
+            <output_collection name="outTables" count="2">
+                <element name="limma-voom_Mut-WT" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
+                        <has_text_matching expression="11304.*0.4573" />
+                    </assert_contents>
+                </element>
+                <element name="limma-voom_WT-Mut" ftype="tabular" >
+                     <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
+                        <has_text_matching expression="11304.*-0.4573" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
     </tests>
 
     <help><![CDATA[
@@ -772,10 +825,17 @@
 *Groups:* The names of the groups for the factor. The names should only contain letters, numbers and underscores, other characters such as spaces and hyphens MUST not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas. If the group names begin with a number an X will be added as a prefix.
 
 **Contrasts of Interest:**
-The contrasts you wish to make between levels.
-A common contrast would be a simple difference between two levels: "Mut-WT"
-represents the difference between the mutant and wild type genotypes.
-Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
+The contrasts you wish to make between levels. A common contrast would be a simple difference between two levels: "Mut-WT"
+represents the difference between the mutant and wild type genotypes. Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used. Alternatively, a tab-separated file can be input that has the names of the comparisons in the first column and one header row, as shown below.
+
+Example:
+
+    ============= =
+    **Contrasts**
+    ------------- -
+    Mut-WT   
+    WT-Mut   
+    ============= =
 
 **Filter Low Counts:**
 Genes with very low counts across all libraries provide little evidence for differential expression.