Mercurial > repos > mingchen0919 > rmarkdown_feature_counts
changeset 6:a2bf35c1974a draft
update
| author | mingchen0919 |
|---|---|
| date | Thu, 28 Dec 2017 16:56:01 -0500 |
| parents | a8ddefbaf55e |
| children | 7857bfd9d604 |
| files | rmarkdown_feature_counts.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/rmarkdown_feature_counts.xml Thu Dec 28 16:49:29 2017 -0500 +++ b/rmarkdown_feature_counts.xml Thu Dec 28 16:56:01 2017 -0500 @@ -72,7 +72,7 @@ optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/> <param type="integer" name="min_mqs" label="minMQS" help="integer giving the minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default." - optional="False"/> + optional="False" value="0"/> <param type="boolean" name="split_only" label="splitOnly" help="logical indicating whether only split alignments (their CIGAR strings contain letter 'N') should be included for summarization. FALSE by default. Example split alignments are exon-spanning reads from RNA-seq data. useMetaFeatures should be set to FALSE and allowMultiOverlap should be set to TRUE, if the purpose of summarization is to assign exon-spanning reads to all their overlapping exons." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/> @@ -87,7 +87,7 @@ optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/> <param type="integer" name="strand_specific" label="strandSpecific" help="integer indicating if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default." - optional="False"/> + optional="False" value="0"/> <param type="boolean" name="junc_counts" label="juncCounts" help="integer indicating if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default." optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>