Mercurial > repos > geert-vandeweyer > cufflinks
changeset 3:1312bf8f5e17 draft
Uploaded
| author | geert-vandeweyer |
|---|---|
| date | Fri, 01 Aug 2014 08:48:32 -0400 |
| parents | e6da12b2440e |
| children | 03fdfb596475 |
| files | cufflinks_wrapper.xml |
| diffstat | 1 files changed, 1 insertions(+), 2 deletions(-) [+] |
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--- a/cufflinks_wrapper.xml Fri Aug 01 08:26:48 2014 -0400 +++ b/cufflinks_wrapper.xml Fri Aug 01 08:48:32 2014 -0400 @@ -8,7 +8,6 @@ <command interpreter="python"> cufflinks_wrapper.py --input=$input - --library-type=$library_type --assembled-isoforms-output=$assembled_isoforms --num-threads="\${GALAXY_SLOTS:-4}" -I $max_intron_len @@ -87,7 +86,7 @@ <when value="No"></when> <when value="Use reference annotation"> <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/> - <param name="compatible_hits_norm" type="select" label="Count hits compatible with reference RNAs only" help="With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped hits used in the FPKM denominator. This option can be combined with -N/--upper-quartile-norm. It is inactive by default, and can only be used in combination with --GTF."> + <param name="compatible_hits_norm" type="select" label="Count hits compatible with reference RNAs only" help="With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped hits used in the FPKM denominator. This option can only be used in combination with --GTF."> <option value="" selected="True">No</option> <option value="--compatible-hits-norm">Yes</option> </param>