Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/coordinatesToSequence.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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-1:000000000000 | 0:e0f8dcca02ed |
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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 </tool> |