# HG changeset patch
# User iuc
# Date 1533331426 14400
# Node ID a416957ee3059a0f6b3c729b750ec3a42e0b81bc
# Parent  9a616afdbda5f34b12e7fc1cce01b57f34084f76
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b

diff -r 9a616afdbda5 -r a416957ee305 deseq2.R
--- a/deseq2.R	Sat May 19 03:55:48 2018 -0400
+++ b/deseq2.R	Fri Aug 03 17:23:46 2018 -0400
@@ -203,7 +203,7 @@
 if (!useTXI & hasHeader) {
     countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
     tbl <- do.call("cbind", countfiles)
-    rownames(sampleTable) <- colnames(tbl) # take sample ids from header
+    colnames(tbl) <- rownames(sampleTable) # take sample ids from header
 
     # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
     oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual",
diff -r 9a616afdbda5 -r a416957ee305 deseq2.xml
--- a/deseq2.xml	Sat May 19 03:55:48 2018 -0400
+++ b/deseq2.xml	Fri Aug 03 17:23:46 2018 -0400
@@ -196,7 +196,7 @@
             <param name="normCounts" value="True"/>
             <output name="counts_out">
                 <assert_contents>
-                    <has_text_matching expression="untreat1\tuntreat2\tuntreat3\tuntreat4\ttreat1\ttreat2\ttreat3" />
+                    <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
                     <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
                 </assert_contents>
             </output>