Mercurial > repos > iuc > deseq2
changeset 16:a416957ee305 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b
| author | iuc |
|---|---|
| date | Fri, 03 Aug 2018 17:23:46 -0400 |
| parents | 9a616afdbda5 |
| children | d9e5cadc7f0b |
| files | deseq2.R deseq2.xml |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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",
--- 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>