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comparison SMART/galaxy/coordinatesToSequence.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="coordinatesToSequence" name="coordinates to sequence"> 1 <tool id="coordinatesToSequence" name="coordinates to sequence">
2 <description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description> 2 <description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1 4 ../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
60 57
61 <outputs> 58 <outputs>
62 <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/> 59 <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
63 </outputs> 60 </outputs>
64 61
65 <help>
66 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.
67 </help>
68 </tool> 62 </tool>