Mercurial > repos > yufei-luo > s_mart
annotate SMART/galaxy/CollapseReads.xml @ 71:d96f6c9a39e0 draft default tip
Removed pyc files.
| author | m-zytnicki |
|---|---|
| date | Thu, 07 Apr 2016 09:25:18 -0400 |
| parents | 1473ab954708 |
| children |
| rev | line source |
|---|---|
| 38 | 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 | |
| 56 | 18 #elif $formatType.FormatInputFileName == 'bam': |
| 19 -f bam | |
| 38 | 20 #elif $formatType.FormatInputFileName == 'gtf': |
| 21 -f gtf | |
| 22 #end if | |
|
69
1473ab954708
Corrected bug in "CollapsedReads" XML file.
m-zytnicki
parents:
56
diff
changeset
|
23 $strand |
| 38 | 24 -o $outputFileGff |
| 25 </command> | |
| 26 | |
| 27 <inputs> | |
| 28 <conditional name="formatType"> | |
| 29 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 30 <option value="bed">bed</option> | |
| 31 <option value="gff">gff</option> | |
| 32 <option value="gff2">gff2</option> | |
| 33 <option value="gff3">gff3</option> | |
| 34 <option value="sam">sam</option> | |
| 56 | 35 <option value="bam">bam</option> |
| 38 | 36 <option value="gtf">gtf</option> |
| 37 </param> | |
| 38 <when value="bed"> | |
| 39 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 40 </when> | |
| 41 <when value="gff"> | |
| 42 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 43 </when> | |
| 44 <when value="gff2"> | |
| 45 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 46 </when> | |
| 47 <when value="gff3"> | |
| 48 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 49 </when> | |
| 50 <when value="sam"> | |
| 51 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
| 52 </when> | |
| 56 | 53 <when value="bam"> |
| 54 <param name="inputFileName" format="bam" type="data" label="Input File"/> | |
| 55 </when> | |
| 38 | 56 <when value="gtf"> |
| 57 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 58 </when> | |
| 59 </conditional> | |
| 60 | |
| 61 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/> | |
| 62 </inputs> | |
| 63 | |
| 64 <outputs> | |
| 65 <data name="outputFileGff" format="gff3"/> | |
| 66 </outputs> | |
| 67 | |
| 68 <help> | |
| 69 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. | |
| 70 | |
| 71 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. | |
| 72 </help> | |
| 73 </tool> |