Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/getExons.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:e0f8dcca02ed |
|---|---|
| 1 <tool id="getExons" name="get exons"> | |
| 2 <description>Get the exons of a set of transcripts.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/getExons.py -i $formatType.inputFileName | |
| 5 #if $formatType.FormatInputFileName == 'bed': | |
| 6 -f bed | |
| 7 #elif $formatType.FormatInputFileName == 'gff': | |
| 8 -f gff | |
| 9 #elif $formatType.FormatInputFileName == 'gff2': | |
| 10 -f gff2 | |
| 11 #elif $formatType.FormatInputFileName == 'gff3': | |
| 12 -f gff3 | |
| 13 #elif $formatType.FormatInputFileName == 'sam': | |
| 14 -f sam | |
| 15 #elif $formatType.FormatInputFileName == 'gtf': | |
| 16 -f gtf | |
| 17 #end if | |
| 18 | |
| 19 #if $optionSelect.Value == "Yes": | |
| 20 -s $optionSelect.selectValue | |
| 21 #end if | |
| 22 | |
| 23 -o $outputFileGff | |
| 24 </command> | |
| 25 | |
| 26 <inputs> | |
| 27 <conditional name="formatType"> | |
| 28 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
| 29 <option value="bed">bed</option> | |
| 30 <option value="gff">gff</option> | |
| 31 <option value="gff2">gff2</option> | |
| 32 <option value="gff3">gff3</option> | |
| 33 <option value="sam">sam</option> | |
| 34 <option value="gtf">gtf</option> | |
| 35 </param> | |
| 36 <when value="bed"> | |
| 37 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
| 38 </when> | |
| 39 <when value="gff"> | |
| 40 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
| 41 </when> | |
| 42 <when value="gff2"> | |
| 43 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
| 44 </when> | |
| 45 <when value="gff3"> | |
| 46 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
| 47 </when> | |
| 48 <when value="sam"> | |
| 49 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
| 50 </when> | |
| 51 <when value="gtf"> | |
| 52 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 | |
| 56 <conditional name="optionSelect"> | |
| 57 <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')"> | |
| 58 <option value="Yes">Yes</option> | |
| 59 <option value="No" selected="true">No</option> | |
| 60 </param> | |
| 61 <when value="Yes"> | |
| 62 <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/> | |
| 63 </when> | |
| 64 <when value="No"> | |
| 65 </when> | |
| 66 </conditional> | |
| 67 </inputs> | |
| 68 | |
| 69 <outputs> | |
| 70 <data format="gff3" name="outputFileGff" label="[getExons -> gff3] Output File"/> | |
| 71 </outputs> | |
| 72 </tool> |