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comparison SMART/galaxy/mappingToCoordinates.xml @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 <tool id="mappingToCoordinates" name="mapping to coordinates">
2 <description>Converts a mapping type file(given by a mapping tool) to a GFF3 type file.</description>
3 <command interpreter="python">
4 ../Java/Python/mappingToCoordinates.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'sam':
8 -f sam
9 #elif $formatType.FormatInputFileName == 'blast -8'
10 -f blast
11 #elif $formatType.FormatInputFileName == 'gff':
12 -f gff
13 #elif $formatType.FormatInputFileName == 'gff2':
14 -f gff2
15 #elif $formatType.FormatInputFileName == 'gff3':
16 -f gff3
17 #end if
18
19 -o $outputFileGff
20 </command>
21
22 <inputs>
23 <conditional name="formatType">
24 <param name="FormatInputFileName" type="select" label="Input File Format">
25 <option value="bed">bed</option>
26 <option value="sam">sam</option>
27 <option value="blast -8">blast</option>
28 <option value="gff">gff</option>
29 <option value="gff2">gff2</option>
30 <option value="gff3">gff3</option>
31 </param>
32 <when value="bed">
33 <param name="inputFileName" format="bed" type="data" label="Input File"/>
34 </when>
35 <when value="sam">
36 <param name="inputFileName" format="sam" type="data" label="Input File"/>
37 </when>
38 <when value="blast -8">
39 <param name="inputFileName" format="blast" type="data" label="Input File"/>
40 </when>
41 <when value="gff">
42 <param name="inputFileName" format="gff" type="data" label="Input File"/>
43 </when>
44 <when value="gff2">
45 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
46 </when>
47 <when value="gff3">
48 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
49 </when>
50 </conditional>
51 </inputs>
52
53 <outputs>
54 <data name="outputFileGff" format="gff3"/>
55 </outputs>
56
57 </tool>