Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/CollapseReads.xml @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
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35:d94018ca4ada | 36:44d5973c188c |
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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> |