annotate SMART/galaxy/CollapseReads.xml @ 18:94ab73e8a190

Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 <tool id="collapseReads" name="collapse reads">
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
2 <description>Merges two genomic features if they have exactly the same genomic coordinates.</description>
18
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
3 <requirements>
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
94ab73e8a190 Uploaded
m-zytnicki
parents: 15
diff changeset
5 </requirements>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 <command interpreter="python">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 ../Java/Python/CollapseReads.py -i $formatType.inputFileName
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 #if $formatType.FormatInputFileName == 'bed':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 -f bed
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #elif $formatType.FormatInputFileName == 'gff':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 -f gff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 #elif $formatType.FormatInputFileName == 'gff2':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 -f gff2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 #elif $formatType.FormatInputFileName == 'gff3':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 -f gff3
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #elif $formatType.FormatInputFileName == 'sam':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 -f sam
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 #elif $formatType.FormatInputFileName == 'gtf':
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 -f gtf
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 #end if
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 -$strand
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 -o $outputFileGff
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 </command>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 <inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 <conditional name="formatType">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 <param name="FormatInputFileName" type="select" label="Input File Format">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 <option value="bed">bed</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 <option value="gff">gff</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 <option value="gff2">gff2</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 <option value="gff3">gff3</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 <option value="sam">sam</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 <option value="gtf">gtf</option>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 </param>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 <when value="bed">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 <when value="gff">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39 <param name="inputFileName" format="gff" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 <when value="gff2">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 <when value="gff3">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
47 <when value="sam">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
48 <param name="inputFileName" format="sam" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
50 <when value="gtf">
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 </when>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53 </conditional>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
55 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 </inputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 <outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 <data name="outputFileGff" format="gff3"/>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 </outputs>
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61
15
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
62 <help>
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
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.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
64
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
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.
440ceca58672 Uploaded
m-zytnicki
parents: 6
diff changeset
66 </help>
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 </tool>