Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/coordinatesToSequence.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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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 <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> |