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comparison SMART/galaxy/getExons.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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>