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comparison SMART/galaxy/changeTagName.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 <tool id="changeTagName" name="change tag name">
2 <description>Change the name of a tag in a GFF file.</description>
3 <command interpreter="python">
4 ../Java/Python/changeTagName.py -i $formatType.inputFileName
5 #elif $formatType.FormatInputFileName == 'gff':
6 -f gff
7 #elif $formatType.FormatInputFileName == 'gff2':
8 -f gff2
9 #elif $formatType.FormatInputFileName == 'gff3':
10 -f gff3
11 #end if
12
13 -t $Tag
14 -n $name
15
16 -o $outputFileGff
17 </command>
18
19 <inputs>
20 <conditional name="formatType">
21 <param name="FormatInputFileName" type="select" label="Input File Format">
22 <option value="gff">gff</option>
23 <option value="gff2">gff2</option>
24 <option value="gff3">gff3</option>
25 </param>
26 <when value="gff">
27 <param name="inputFileName" format="gff" type="data" label="Input File"/>
28 </when>
29 <when value="gff2">
30 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
31 </when>
32 <when value="gff3">
33 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
34 </when>
35 </conditional>
36
37 <param name="Tag" type="text" label="tag option" help="The tag you want to change"/>
38 <param name="name" type="text" label="name option" help="A new name for the tag"/>
39 </inputs>
40
41 <outputs>
42 <data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/>
43 </outputs>
44
45 <help>
46 Change the name of a tag in the 9th field of a GFF3 file (please consult http://www.sequenceontology.org/gff3.shtml to know more about this format).
47 </help>
48 </tool>