Mercurial > repos > iuc > dexseq
changeset 3:f89c9b25feb4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e785d126b23609208b055fb8902f3b9368e9b839
| author | iuc |
|---|---|
| date | Sat, 28 Jul 2018 03:44:02 -0400 |
| parents | 6e8b61c54ff3 |
| children | 251393b72616 |
| files | dexseq_count.xml test-data/in.bam test-data/out_count.tab |
| diffstat | 3 files changed, 229 insertions(+), 0 deletions(-) [+] |
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--- a/dexseq_count.xml Sun Jan 28 04:04:39 2018 -0500 +++ b/dexseq_count.xml Sat Jul 28 03:44:02 2018 -0400 @@ -78,6 +78,13 @@ <param name="aggregate" value="True"/> <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/> </test> + <!-- Ensure count mode works --> + <test> + <param name="mode_select" value="count" /> + <param name="bamfile" ftype="bam" value="in.bam" /> + <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/> + <output name="counts_file" ftype="tabular" file="out_count.tab"/> + </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_count.tab Sat Jul 28 03:44:02 2018 -0400 @@ -0,0 +1,222 @@ +FBgn0001313:001 0 +FBgn0001313:002 0 +FBgn0001313:003 0 +FBgn0001313:004 0 +FBgn0001313:005 0 +FBgn0001313:006 0 +FBgn0001313:007 0 +FBgn0001313:008 0 +FBgn0001313:009 0 +FBgn0001313:010 0 +FBgn0001313:011 0 +FBgn0001314:001 0 +FBgn0001314:002 0 +FBgn0001314:003 0 +FBgn0001314:004 0 +FBgn0001314:005 0 +FBgn0001314:006 0 +FBgn0001314:007 0 +FBgn0001314:008 0 +FBgn0001314:009 0 +FBgn0001315:001 0 +FBgn0001315:002 0 +FBgn0001315:003 0 +FBgn0001315:004 0 +FBgn0001315:005 0 +FBgn0001315:006 0 +FBgn0001315:007 0 +FBgn0001315:008 0 +FBgn0001315:009 0 +FBgn0001315:010 0 +FBgn0001315:011 0 +FBgn0001315:012 0 +FBgn0001315:013 0 +FBgn0001315:014 0 +FBgn0001315:015 0 +FBgn0003559:001 0 +FBgn0003559:002 0 +FBgn0003559:003 0 +FBgn0003559:004 0 +FBgn0003559:005 0 +FBgn0003559:006 0 +FBgn0003559:007 0 +FBgn0003559:008 0 +FBgn0003559:009 0 +FBgn0003559:010 0 +FBgn0003559:011 0 +FBgn0003559:012 0 +FBgn0003559:013 0 +FBgn0003559:014 0 +FBgn0003559:015 0 +FBgn0003559:016 0 +FBgn0003559:017 0 +FBgn0004607:001 0 +FBgn0004607:002 0 +FBgn0004607:003 0 +FBgn0004607:004 0 +FBgn0004607:005 0 +FBgn0004607:006 0 +FBgn0004607:007 0 +FBgn0004607:008 0 +FBgn0004607:009 0 +FBgn0004607:010 0 +FBgn0004607:011 0 +FBgn0004607:012 0 +FBgn0004607:013 0 +FBgn0004607:014 0 +FBgn0004607:015 0 +FBgn0004607:016 0 +FBgn0004607:017 0 +FBgn0004607:018 0 +FBgn0004859:001 0 +FBgn0004859:002 0 +FBgn0004859:003 0 +FBgn0004859:004 0 +FBgn0004859:005 0 +FBgn0004859:006 0 +FBgn0004859:007 0 +FBgn0004859:008 0 +FBgn0004859:009 0 +FBgn0005558:001 0 +FBgn0005558:002 0 +FBgn0005558:003 0 +FBgn0005558:004 0 +FBgn0005558:005 0 +FBgn0005558:006 0 +FBgn0005558:007 0 +FBgn0005558:008 0 +FBgn0005558:009 0 +FBgn0005558:010 0 +FBgn0005558:011 0 +FBgn0005561:001 0 +FBgn0005561:002 0 +FBgn0005561:003 0 +FBgn0005561:004 0 +FBgn0005561:005 0 +FBgn0005561:006 0 +FBgn0005561:007 0 +FBgn0005561:008 0 +FBgn0005561:009 0 +FBgn0005561:010 0 +FBgn0005561:011 0 +FBgn0005561:012 0 +FBgn0005561:013 0 +FBgn0005666:001 0 +FBgn0005666:002 0 +FBgn0005666:003 0 +FBgn0005666:004 0 +FBgn0005666:005 0 +FBgn0005666:006 0 +FBgn0005666:007 0 +FBgn0005666:008 0 +FBgn0005666:009 0 +FBgn0005666:010 0 +FBgn0005666:011 0 +FBgn0005666:012 0 +FBgn0005666:013 0 +FBgn0005666:014 0 +FBgn0005666:015 0 +FBgn0005666:016 0 +FBgn0005666:017 0 +FBgn0005666:018 0 +FBgn0005666:019 0 +FBgn0005666:020 0 +FBgn0005666:021 0 +FBgn0005666:022 0 +FBgn0005666:023 0 +FBgn0005666:024 0 +FBgn0005666:025 0 +FBgn0005666:026 0 +FBgn0005666:027 0 +FBgn0005666:028 0 +FBgn0005666:029 0 +FBgn0005666:030 0 +FBgn0005666:031 0 +FBgn0005666:032 0 +FBgn0005666:033 0 +FBgn0005666:034 0 +FBgn0005666:035 0 +FBgn0005666:036 0 +FBgn0005666:037 0 +FBgn0005666:038 0 +FBgn0005666:039 0 +FBgn0005666:040 0 +FBgn0005666:041 0 +FBgn0005666:042 0 +FBgn0005666:043 0 +FBgn0005666:044 0 +FBgn0005666:045 0 +FBgn0005666:046 0 +FBgn0005666:047 0 +FBgn0010217:001 0 +FBgn0010217:002 0 +FBgn0010217:003 0 +FBgn0010217:004 0 +FBgn0010217:005 0 +FBgn0010217:006 0 +FBgn0010217:007 0 +FBgn0011642:001 0 +FBgn0011642:002 0 +FBgn0011642:003 0 +FBgn0011642:004 0 +FBgn0011642:005 0 +FBgn0011642:006 0 +FBgn0011642:007 0 +FBgn0011642:008 0 +FBgn0011642:009 0 +FBgn0011642:010 0 +FBgn0011642:011 0 +FBgn0011642:012 0 +FBgn0011642:013 0 +FBgn0011642:014 0 +FBgn0011642:015 0 +FBgn0011642:016 0 +FBgn0011642:017 0 +FBgn0011642:018 0 +FBgn0011642:019 0 +FBgn0011747:001 0 +FBgn0011747:002 0 +FBgn0011747:003 0 +FBgn0011747:004 0 +FBgn0011747:005 0 +FBgn0011747:006 0 +FBgn0011747:007 0 +FBgn0011747:008 0 +FBgn0011747:009 0 +FBgn0011747:010 0 +FBgn0011747:011 0 +FBgn0011747:012 0 +FBgn0011747:013 0 +FBgn0013674:001 0 +FBgn0013675:001 0 +FBgn0013678:001 0 +FBgn0013679:001 0 +FBgn0013681:001 0 +FBgn0013684:001 0 +FBgn0013685:001 0 +FBgn0013688:001 0 +FBgn0013689:001 0 +FBgn0013690:001 0 +FBgn0013691:001 0 +FBgn0013692:001 0 +FBgn0013693:001 0 +FBgn0013694:001 0 +FBgn0013695:001 0 +FBgn0013696:001 0 +FBgn0013697:001 0 +FBgn0013698:001 0 +FBgn0013699:001 0 +FBgn0013700:001 0 +FBgn0013701:001 0 +FBgn0013702:001 0 +FBgn0013703:001 0 +FBgn0013704:001 0 +FBgn0013705:001 0 +FBgn0013706:001 0 +FBgn0013707:001 0 +FBgn0013710:001 0 +_ambiguous 0 +_ambiguous_readpair_position 0 +_empty 0 +_lowaqual 0 +_notaligned 0