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comparison SMART/galaxy/test/CollapseReads.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 769e306b7933
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17:b0e8584489e6 18:94ab73e8a190
1 <tool id="collapseReads" name="collapseReads">
2 <description>Merges two reads if they have exactly the same genomic coordinates.</description>
3 <command interpreter="python">
4 ../Java/Python/CollapseReads.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 $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #end if
14
15 -$strand
16 -o $outputFileGff
17 --galaxy
18 </command>
19
20 <inputs>
21 <conditional name="formatType">
22 <param name="FormatInputFileName" type="select" label="Input File Format">
23 <option value="bed">bed</option>
24 <option value="gff">gff</option>
25 <option value="gff2">gff2</option>
26 <option value="gff3">gff3</option>
27 </param>
28 <when value="bed">
29 <param name="inputFileName" format="bed" type="data" label="Input File"/>
30 </when>
31 <when value="gff">
32 <param name="inputFileName" format="gff" type="data" label="Input File"/>
33 </when>
34 <when value="gff2">
35 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
36 </when>
37 <when value="gff3">
38 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
39 </when>
40 </conditional>
41
42 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/>
43 </inputs>
44
45 <outputs>
46 <data name="outputFileGff" format="gff3"/>
47 </outputs>
48
49 </tool>