Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/changeTagName.xml @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
parents | |
children | 440ceca58672 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 <tool id="changeTagName" name="change tag name"> | |
2 <description>Changes the name of tag of a list of transcripts.</description> | |
3 <command interpreter="python"> | |
4 ../Java/Python/changeTagName.py -i $formatType.inputFileName | |
5 #if $formatType.FormatInputFileName == 'bed': | |
6 -f bed | |
7 #elif $formatType.FormatInputFileName == 'gff': | |
8 -f gff | |
9 #elif $formatType.FormatInputFileName == 'gff2': | |
10 -f gff2 | |
11 #elif $formatType.FormatInputFileName == 'gff3': | |
12 -f gff3 | |
13 #end if | |
14 | |
15 -t $Tag | |
16 -n $name | |
17 | |
18 -o $outputFileGff | |
19 </command> | |
20 | |
21 <inputs> | |
22 <conditional name="formatType"> | |
23 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
24 <option value="bed">bed</option> | |
25 <option value="gff">gff</option> | |
26 <option value="gff2">gff2</option> | |
27 <option value="gff3">gff3</option> | |
28 </param> | |
29 <when value="bed"> | |
30 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
31 </when> | |
32 <when value="gff"> | |
33 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
34 </when> | |
35 <when value="gff2"> | |
36 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
37 </when> | |
38 <when value="gff3"> | |
39 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
40 </when> | |
41 </conditional> | |
42 | |
43 <param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/> | |
44 <param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/> | |
45 | |
46 | |
47 | |
48 </inputs> | |
49 | |
50 <outputs> | |
51 <data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/> | |
52 </outputs> | |
53 | |
54 </tool> |