comparison SMART/galaxy/CollapseReads.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="collapseReads" name="collapse reads">
2 <description>Merges two genomic features 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 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName == 'gtf':
16 -f gtf
17 #end if
18 -$strand
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="gff">gff</option>
27 <option value="gff2">gff2</option>
28 <option value="gff3">gff3</option>
29 <option value="sam">sam</option>
30 <option value="gtf">gtf</option>
31 </param>
32 <when value="bed">
33 <param name="inputFileName" format="bed" type="data" label="Input File"/>
34 </when>
35 <when value="gff">
36 <param name="inputFileName" format="gff" type="data" label="Input File"/>
37 </when>
38 <when value="gff2">
39 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
40 </when>
41 <when value="gff3">
42 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
43 </when>
44 <when value="sam">
45 <param name="inputFileName" format="sam" type="data" label="Input File"/>
46 </when>
47 <when value="gtf">
48 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
49 </when>
50 </conditional>
51
52 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/>
53 </inputs>
54
55 <outputs>
56 <data name="outputFileGff" format="gff3"/>
57 </outputs>
58
59 <help>
60 Merge two input genomic coordinates iff they are exactly the same. If two or more genomic coordinates are merged, the tag **nbElements** is updated accordingly. As a consequence, all the reads which are exactly the same appear as one genomic coordinate.
61
62 This is especially useful for short RNA sequencing (where you want to count the number of read per miRNA, siRNA, etc.) or 5' capped short reads.
63 </help>
64 </tool>