Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/CollapseReads.xml @ 56:97aa2e42bfdf
Uploaded
| author | m-zytnicki |
|---|---|
| date | Wed, 05 Feb 2014 11:51:11 -0500 |
| parents | 2c0c0a89fad7 |
| children | 1473ab954708 |
comparison
equal
deleted
inserted
replaced
| 55:2ac71607aa60 | 56:97aa2e42bfdf |
|---|---|
| 13 -f gff2 | 13 -f gff2 |
| 14 #elif $formatType.FormatInputFileName == 'gff3': | 14 #elif $formatType.FormatInputFileName == 'gff3': |
| 15 -f gff3 | 15 -f gff3 |
| 16 #elif $formatType.FormatInputFileName == 'sam': | 16 #elif $formatType.FormatInputFileName == 'sam': |
| 17 -f sam | 17 -f sam |
| 18 #elif $formatType.FormatInputFileName == 'bam': | |
| 19 -f bam | |
| 18 #elif $formatType.FormatInputFileName == 'gtf': | 20 #elif $formatType.FormatInputFileName == 'gtf': |
| 19 -f gtf | 21 -f gtf |
| 20 #end if | 22 #end if |
| 21 -$strand | 23 -$strand |
| 22 -o $outputFileGff | 24 -o $outputFileGff |
| 28 <option value="bed">bed</option> | 30 <option value="bed">bed</option> |
| 29 <option value="gff">gff</option> | 31 <option value="gff">gff</option> |
| 30 <option value="gff2">gff2</option> | 32 <option value="gff2">gff2</option> |
| 31 <option value="gff3">gff3</option> | 33 <option value="gff3">gff3</option> |
| 32 <option value="sam">sam</option> | 34 <option value="sam">sam</option> |
| 35 <option value="bam">bam</option> | |
| 33 <option value="gtf">gtf</option> | 36 <option value="gtf">gtf</option> |
| 34 </param> | 37 </param> |
| 35 <when value="bed"> | 38 <when value="bed"> |
| 36 <param name="inputFileName" format="bed" type="data" label="Input File"/> | 39 <param name="inputFileName" format="bed" type="data" label="Input File"/> |
| 37 </when> | 40 </when> |
| 44 <when value="gff3"> | 47 <when value="gff3"> |
| 45 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | 48 <param name="inputFileName" format="gff3" type="data" label="Input File"/> |
| 46 </when> | 49 </when> |
| 47 <when value="sam"> | 50 <when value="sam"> |
| 48 <param name="inputFileName" format="sam" type="data" label="Input File"/> | 51 <param name="inputFileName" format="sam" type="data" label="Input File"/> |
| 52 </when> | |
| 53 <when value="bam"> | |
| 54 <param name="inputFileName" format="bam" type="data" label="Input File"/> | |
| 49 </when> | 55 </when> |
| 50 <when value="gtf"> | 56 <when value="gtf"> |
| 51 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | 57 <param name="inputFileName" format="gtf" type="data" label="Input File"/> |
| 52 </when> | 58 </when> |
| 53 </conditional> | 59 </conditional> |