comparison SMART/galaxy/CollapseReads.xml @ 38:2c0c0a89fad7

Uploaded
author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
parents
children 97aa2e42bfdf
comparison
equal deleted inserted replaced
37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="collapseReads" name="collapse reads">
2 <description>Merges two genomic features if they have exactly the same genomic coordinates.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/CollapseReads.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName == 'gff':
11 -f gff
12 #elif $formatType.FormatInputFileName == 'gff2':
13 -f gff2
14 #elif $formatType.FormatInputFileName == 'gff3':
15 -f gff3
16 #elif $formatType.FormatInputFileName == 'sam':
17 -f sam
18 #elif $formatType.FormatInputFileName == 'gtf':
19 -f gtf
20 #end if
21 -$strand
22 -o $outputFileGff
23 </command>
24
25 <inputs>
26 <conditional name="formatType">
27 <param name="FormatInputFileName" type="select" label="Input File Format">
28 <option value="bed">bed</option>
29 <option value="gff">gff</option>
30 <option value="gff2">gff2</option>
31 <option value="gff3">gff3</option>
32 <option value="sam">sam</option>
33 <option value="gtf">gtf</option>
34 </param>
35 <when value="bed">
36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
37 </when>
38 <when value="gff">
39 <param name="inputFileName" format="gff" type="data" label="Input File"/>
40 </when>
41 <when value="gff2">
42 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
43 </when>
44 <when value="gff3">
45 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
46 </when>
47 <when value="sam">
48 <param name="inputFileName" format="sam" type="data" label="Input File"/>
49 </when>
50 <when value="gtf">
51 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
52 </when>
53 </conditional>
54
55 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/>
56 </inputs>
57
58 <outputs>
59 <data name="outputFileGff" format="gff3"/>
60 </outputs>
61
62 <help>
63 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.
64
65 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.
66 </help>
67 </tool>