# HG changeset patch
# User iuc
# Date 1565261029 14400
# Node ID 47094543a5ff4f6afb6a5680394069d4025e8b0e
# Parent  7cf6248bc1739efbd11810ff367f9deb4ace679a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36

diff -r 7cf6248bc173 -r 47094543a5ff edger.xml
--- a/edger.xml	Sat Feb 09 07:19:54 2019 -0500
+++ b/edger.xml	Thu Aug 08 06:43:49 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="edger" name="edgeR" version="3.24.1">
+<tool id="edger" name="edgeR" version="3.24.1+galaxy1">
     <description>
         Perform differential expression of count data
     </description>
@@ -175,9 +175,9 @@
 
         <!-- 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 more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
+            <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. (MT.t1-MT.t0)-(WT.t1-WT.t0). 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 or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons.">
                 <validator type="empty_field" />
-                <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
+                <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator>
             </param>
         </repeat>
 
@@ -309,6 +309,35 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Complex contrasts constructions -->
+        <test>
+            <param name="format" value="matrix" />
+            <param name="counts" value="matrix-complex.txt" />
+            <repeat name="rep_factor">
+                <param name="factorName" value="Genotype"/>
+                <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB" />
+            </repeat>
+            <repeat name="rep_contrast">
+                <param name="contrast" value="(MutA-MutB)-(WTA-WTB)" />
+            </repeat>
+            <param name="normalisationOption" value="TMM" />
+            <output_collection name="outTables" count="1">
+                <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular" >
+                    <assert_contents>
+                        <has_text_matching expression="GeneID.*logFC.*logCPM.*F.*PValue.*FDR" />
+                        <has_text_matching expression="11304.*15.53" />
+                   </assert_contents>
+               </element>
+            </output_collection>
+            <output name="outReport" >
+                <assert_contents>
+                    <has_text text="edgeR Analysis Output" />
+                    <has_text text="quasi-likelihood" />
+                    <not_has_text text="likelihood ratio" />
+                    <not_has_text text="RData" />
+                </assert_contents>
+            </output>
+        </test>
         <!-- Ensure annotation file input works -->
         <test>
             <param name="format" value="matrix" />
diff -r 7cf6248bc173 -r 47094543a5ff test-data/matrix-complex.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix-complex.txt	Thu Aug 08 06:43:49 2019 -0400
@@ -0,0 +1,7 @@
+GeneID	MutA1	MutA2	MutA3	MutB1	MutB2	MutB3	WTA1	WTA2	WTA3	WTB1	WTB2	WTB3
+11287	1463	1441	1495	1463	1441	1495	1699	1528	1601	1699	1528	1601
+11298	1345	1291	1346	1345	1291	1346	1905	1744	1834	1905	1744	1834
+11302	5	6	5	5	6	5	6	8	7	6	8	7
+11303	1574	1519	1654	1574	1519	1654	2099	1974	2100	2099	1974	2100
+11304	361	397	346	361	397	346	356	312	337	356	312	337
+11305	1762	1942	2027	1762	1942	2027	2528	2438	2493	2528	2438	2493