Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/CollapseReads.xml @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
| parents | |
| children | 97aa2e42bfdf |
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| 37:d22fadc825e3 | 38:2c0c0a89fad7 |
|---|---|
| 1 <tool id="collapseReads" name="collapse reads"> | |
| 2 <description>Merges two genomic features if they have exactly the same genomic coordinates.</description> | |
| 3 <requirements> | |
| 4 <requirement type="set_environment">PYTHONPATH</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 ../Java/Python/CollapseReads.py -i $formatType.inputFileName | |
| 8 #if $formatType.FormatInputFileName == 'bed': | |
| 9 -f bed | |
| 10 #elif $formatType.FormatInputFileName == 'gff': | |
| 11 -f gff | |
| 12 #elif $formatType.FormatInputFileName == 'gff2': | |
| 13 -f gff2 | |
| 14 #elif $formatType.FormatInputFileName == 'gff3': | |
| 15 -f gff3 | |
| 16 #elif $formatType.FormatInputFileName == 'sam': | |
| 17 -f sam | |
| 18 #elif $formatType.FormatInputFileName == 'gtf': | |
| 19 -f gtf | |
| 20 #end if | |
| 21 -$strand | |
| 22 -o $outputFileGff | |
| 23 </command> | |
| 24 | |
| 25 <inputs> | |
| 26 <conditional name="formatType"> | |
| 27 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 28 <option value="bed">bed</option> | |
| 29 <option value="gff">gff</option> | |
| 30 <option value="gff2">gff2</option> | |
| 31 <option value="gff3">gff3</option> | |
| 32 <option value="sam">sam</option> | |
| 33 <option value="gtf">gtf</option> | |
| 34 </param> | |
| 35 <when value="bed"> | |
| 36 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 37 </when> | |
| 38 <when value="gff"> | |
| 39 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 40 </when> | |
| 41 <when value="gff2"> | |
| 42 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 43 </when> | |
| 44 <when value="gff3"> | |
| 45 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 46 </when> | |
| 47 <when value="sam"> | |
| 48 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
| 49 </when> | |
| 50 <when value="gtf"> | |
| 51 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 | |
| 55 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/> | |
| 56 </inputs> | |
| 57 | |
| 58 <outputs> | |
| 59 <data name="outputFileGff" format="gff3"/> | |
| 60 </outputs> | |
| 61 | |
| 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> |