|
6
|
1 <tool id="coordinatesToSequence" name="coordinates to sequence">
|
|
|
2 <description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
|
|
18
|
3 <requirements>
|
|
|
4 <requirement type="set_environment">PYTHONPATH</requirement>
|
|
|
5 </requirements>
|
|
6
|
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
|
|
15
|
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>
|
|
6
|
68 </tool>
|
