Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CollapseReads.xml @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 <tool id="collapseReads" name="collapse reads"> 1 <tool id="collapseReads" name="collapse reads">
2 <description>Merges two genomic features if they have exactly the same genomic coordinates.</description> 2 <description>Merges two reads if they have exactly the same genomic coordinates.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/CollapseReads.py -i $formatType.inputFileName 4 ../Java/Python/CollapseReads.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
50 <when value="gtf"> 47 <when value="gtf">
51 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 48 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
52 </when> 49 </when>
53 </conditional> 50 </conditional>
54 51
55 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/> 52 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/>
56 </inputs> 53 </inputs>
57 54
58 <outputs> 55 <outputs>
59 <data name="outputFileGff" format="gff3"/> 56 <data name="outputFileGff" format="gff3"/>
60 </outputs> 57 </outputs>
61 58
62 <help>
63 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.
64
65 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.
66 </help>
67 </tool> 59 </tool>