Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getExons.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="getExons" name="get exons"> | |
2 <description>Get the exons of a set of transcripts.</description> | |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 ../Java/Python/getExons.py -i $formatType.inputFileName | |
8 #if $formatType.FormatInputFileName == 'bed': | |
9 -f bed | |
10 #elif $formatType.FormatInputFileName == 'gff': | |
11 -f gff | |
12 #elif $formatType.FormatInputFileName == 'gff2': | |
13 -f gff2 | |
14 #elif $formatType.FormatInputFileName == 'gff3': | |
15 -f gff3 | |
16 #elif $formatType.FormatInputFileName == 'sam': | |
17 -f sam | |
18 #elif $formatType.FormatInputFileName == 'gtf': | |
19 -f gtf | |
20 #end if | |
21 | |
22 #if $optionSelect.Value == "Yes": | |
23 -s $optionSelect.selectValue | |
24 #end if | |
25 | |
26 -o $outputFileGff | |
27 </command> | |
28 | |
29 <inputs> | |
30 <conditional name="formatType"> | |
31 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
32 <option value="bed">bed</option> | |
33 <option value="gff">gff</option> | |
34 <option value="gff2">gff2</option> | |
35 <option value="gff3">gff3</option> | |
36 <option value="sam">sam</option> | |
37 <option value="gtf">gtf</option> | |
38 </param> | |
39 <when value="bed"> | |
40 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
41 </when> | |
42 <when value="gff"> | |
43 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
44 </when> | |
45 <when value="gff2"> | |
46 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
47 </when> | |
48 <when value="gff3"> | |
49 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
50 </when> | |
51 <when value="sam"> | |
52 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
53 </when> | |
54 <when value="gtf"> | |
55 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
56 </when> | |
57 </conditional> | |
58 | |
59 <conditional name="optionSelect"> | |
60 <param name="Value" type="select" label="select some of the exons (like '1,2,5..-3,-1')"> | |
61 <option value="Yes">Yes</option> | |
62 <option value="No" selected="true">No</option> | |
63 </param> | |
64 <when value="Yes"> | |
65 <param name="selectValue" type="text" value="None" label="select option" help="like '1,2,5..-3,-1'"/> | |
66 </when> | |
67 <when value="No"> | |
68 </when> | |
69 </conditional> | |
70 </inputs> | |
71 | |
72 <outputs> | |
73 <data format="gff3" name="outputFileGff" label="[get exons] output file"/> | |
74 </outputs> | |
75 <tests> | |
76 <test> | |
77 <param name="FormatInputFileName" value="gtf" /> | |
78 <param name="inputFileName" value="genes.gtf" /> | |
79 <param name="Value" value="No"/> | |
80 <output name="outputFileGff" file="exp_getExons.gff3" /> | |
81 </test> | |
82 </tests> | |
83 | |
84 <help> | |
85 Provide all the exons of an annotation file. | |
86 </help> | |
87 </tool> |