Mercurial > repos > yufei-luo > s_mart
diff SMART/galaxy/CollapseReads.xml @ 15:440ceca58672
Uploaded
author | m-zytnicki |
---|---|
date | Mon, 22 Apr 2013 11:08:07 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
line wrap: on
line diff
--- a/SMART/galaxy/CollapseReads.xml Fri Apr 19 10:13:11 2013 -0400 +++ b/SMART/galaxy/CollapseReads.xml Mon Apr 22 11:08:07 2013 -0400 @@ -1,5 +1,5 @@ <tool id="collapseReads" name="collapse reads"> - <description>Merges two reads if they have exactly the same genomic coordinates.</description> + <description>Merges two genomic features if they have exactly the same genomic coordinates.</description> <command interpreter="python"> ../Java/Python/CollapseReads.py -i $formatType.inputFileName #if $formatType.FormatInputFileName == 'bed': @@ -49,11 +49,16 @@ </when> </conditional> - <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/> + <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/> </inputs> <outputs> <data name="outputFileGff" format="gff3"/> </outputs> + <help> +Merge two input genomic coordinates iff they are exactly the same. If two or more genomic coordinates are merged, the tag **nbElements** is updated accordingly. As a consequence, all the reads which are exactly the same appear as one genomic coordinate. + +This is especially useful for short RNA sequencing (where you want to count the number of read per miRNA, siRNA, etc.) or 5' capped short reads. + </help> </tool>