Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/coordinatesToSequence.xml @ 36:44d5973c188c
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 15:02:29 -0400 |
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| 35:d94018ca4ada | 36:44d5973c188c |
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| 1 <tool id="coordinatesToSequence" name="coordinates to sequence"> | |
| 2 <description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description> | |
| 3 <command interpreter="python"> | |
| 4 ../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1 | |
| 5 #if $formatType.FormatInputFileName1 == 'bed': | |
| 6 -f bed | |
| 7 #elif $formatType.FormatInputFileName1 == 'gff': | |
| 8 -f gff | |
| 9 #elif $formatType.FormatInputFileName1 == 'gff2': | |
| 10 -f gff2 | |
| 11 #elif $formatType.FormatInputFileName1 == 'gff3': | |
| 12 -f gff3 | |
| 13 #elif $formatType.FormatInputFileName1 == 'sam': | |
| 14 -f sam | |
| 15 #elif $formatType.FormatInputFileName1 == 'gtf': | |
| 16 -f gtf | |
| 17 #end if | |
| 18 | |
| 19 -s $sequence | |
| 20 -o $outputFileFasta | |
| 21 | |
| 22 </command> | |
| 23 | |
| 24 <inputs> | |
| 25 <conditional name="formatType"> | |
| 26 <param name="FormatInputFileName1" type="select" label="Input File Format"> | |
| 27 <option value="bed">bed</option> | |
| 28 <option value="gff">gff</option> | |
| 29 <option value="gff2">gff2</option> | |
| 30 <option value="gff3">gff3</option> | |
| 31 <option value="sam">sam</option> | |
| 32 <option value="gtf">gtf</option> | |
| 33 </param> | |
| 34 <when value="bed"> | |
| 35 <param name="inputFileName1" format="bed" type="data" label="Input File"/> | |
| 36 </when> | |
| 37 <when value="gff"> | |
| 38 <param name="inputFileName1" format="gff" type="data" label="Input File"/> | |
| 39 </when> | |
| 40 <when value="gff2"> | |
| 41 <param name="inputFileName1" format="gff2" type="data" label="Input File"/> | |
| 42 </when> | |
| 43 <when value="gff3"> | |
| 44 <param name="inputFileName1" format="gff3" type="data" label="Input File"/> | |
| 45 </when> | |
| 46 <when value="sam"> | |
| 47 <param name="inputFileName1" format="sam" type="data" label="Input File"/> | |
| 48 </when> | |
| 49 <when value="gtf"> | |
| 50 <param name="inputFileName1" format="gtf" type="data" label="Input File"/> | |
| 51 </when> | |
| 52 </conditional> | |
| 53 | |
| 54 <param name="sequence" type="data" label="Reference fasta File" format="fasta"/> | |
| 55 | |
| 56 </inputs> | |
| 57 | |
| 58 <outputs> | |
| 59 <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/> | |
| 60 </outputs> | |
| 61 | |
| 62 <help> | |
| 63 You can use this tool, if you just want to convert your mapping data to genomic coordinates, without any filtering. It requires a genomic coordinates file together with its format, an output format (GFF3, BED, etc...), the genome, and prints you the corresponding file. | |
| 64 </help> | |
| 65 </tool> |