Mercurial > repos > m-zytnicki > mmquant
changeset 2:fc9d40c697e8 draft
Uploaded
| author | m-zytnicki |
|---|---|
| date | Tue, 11 Apr 2017 11:26:53 -0400 |
| parents | 87c5fa8651c1 |
| children | 6de4f428ef5f |
| files | mmquant.xml |
| diffstat | 1 files changed, 9 insertions(+), 11 deletions(-) [+] |
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--- a/mmquant.xml Wed Feb 15 06:03:00 2017 -0500 +++ b/mmquant.xml Tue Apr 11 11:26:53 2017 -0400 @@ -6,7 +6,7 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ - mmquant + mmquant_static -a "$annotation" -r #for $r in $reads_info @@ -20,6 +20,10 @@ #for $r in $reads_info ${r.strand} #end for + -t + #for $r in $reads_info + ${r.sorted} + #end for -n #for $r in $reads_info ${r.name} @@ -44,6 +48,10 @@ <option value="F">forward (for single-end reads)</option> <option value="R">reverse (for single-end reads)</option> </param> + <param name="sorted" type="select" label="Sorted" multiple="false" > + <option value="Y" selected="yes">yes</option> + <option value="N">no</option> + </param> </repeat> <param name="overlap" type="float" value="-1" label="Overlap type" help="<0: read is included, <1: overlap, otherwise: # nt" /> <param name="gene_name" type="boolean" label="Print gene name instead of IDs" truevalue="-g" falsevalue="" help="use gene name instead of gene ID in the output file" /> @@ -78,16 +86,6 @@ .. _article: http://www.genomebiology.com/2015/16/1/177 -**Strands** - -Strands can be: - -* for paired-end reads: ``U`` (unknown), ``FR`` (forward-reverse), ``RF`` (reverse-forward), ``FF`` (forward-forward); - -* for single-end reads: ``U`` (unknown), ``F`` (forward), ``R`` (reverse); - -* Default: ``U``. - **Annotation file**