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comparison SMART/galaxy/CollapseReads.xml @ 15:440ceca58672

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author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
1 <tool id="collapseReads" name="collapse reads"> 1 <tool id="collapseReads" name="collapse reads">
2 <description>Merges two reads if they have exactly the same genomic coordinates.</description> 2 <description>Merges two genomic features if they have exactly the same genomic coordinates.</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 ../Java/Python/CollapseReads.py -i $formatType.inputFileName 4 ../Java/Python/CollapseReads.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed': 5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed 6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff': 7 #elif $formatType.FormatInputFileName == 'gff':
47 <when value="gtf"> 47 <when value="gtf">
48 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 48 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
49 </when> 49 </when>
50 </conditional> 50 </conditional>
51 51
52 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/> 52 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/>
53 </inputs> 53 </inputs>
54 54
55 <outputs> 55 <outputs>
56 <data name="outputFileGff" format="gff3"/> 56 <data name="outputFileGff" format="gff3"/>
57 </outputs> 57 </outputs>
58 58
59 <help>
60 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.
61
62 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.
63 </help>
59 </tool> 64 </tool>