38
+ − 1 <tool id="coordinatesToSequence" name="coordinates to sequence">
+ − 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">
+ − 7 ../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1
+ − 8 #if $formatType.FormatInputFileName1 == 'bed':
+ − 9 -f bed
+ − 10 #elif $formatType.FormatInputFileName1 == 'gff':
+ − 11 -f gff
+ − 12 #elif $formatType.FormatInputFileName1 == 'gff2':
+ − 13 -f gff2
+ − 14 #elif $formatType.FormatInputFileName1 == 'gff3':
+ − 15 -f gff3
+ − 16 #elif $formatType.FormatInputFileName1 == 'sam':
+ − 17 -f sam
+ − 18 #elif $formatType.FormatInputFileName1 == 'gtf':
+ − 19 -f gtf
+ − 20 #end if
+ − 21
+ − 22 -s $sequence
+ − 23 -o $outputFileFasta
+ − 24
+ − 25 </command>
+ − 26
+ − 27 <inputs>
+ − 28 <conditional name="formatType">
+ − 29 <param name="FormatInputFileName1" 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>
+ − 35 <option value="gtf">gtf</option>
+ − 36 </param>
+ − 37 <when value="bed">
+ − 38 <param name="inputFileName1" format="bed" type="data" label="Input File"/>
+ − 39 </when>
+ − 40 <when value="gff">
+ − 41 <param name="inputFileName1" format="gff" type="data" label="Input File"/>
+ − 42 </when>
+ − 43 <when value="gff2">
+ − 44 <param name="inputFileName1" format="gff2" type="data" label="Input File"/>
+ − 45 </when>
+ − 46 <when value="gff3">
+ − 47 <param name="inputFileName1" format="gff3" type="data" label="Input File"/>
+ − 48 </when>
+ − 49 <when value="sam">
+ − 50 <param name="inputFileName1" format="sam" type="data" label="Input File"/>
+ − 51 </when>
+ − 52 <when value="gtf">
+ − 53 <param name="inputFileName1" format="gtf" type="data" label="Input File"/>
+ − 54 </when>
+ − 55 </conditional>
+ − 56
+ − 57 <param name="sequence" type="data" label="Reference fasta File" format="fasta"/>
+ − 58
+ − 59 </inputs>
+ − 60
+ − 61 <outputs>
+ − 62 <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
+ − 63 </outputs>
+ − 64
+ − 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>