Mercurial > repos > jjohnson > filter_bed_on_splice_junctions
comparison filter_bed_on_splice_junctions.xml @ 0:915e5c5e02e6 draft default tip
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author | jjohnson |
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date | Wed, 05 Feb 2014 08:18:49 -0500 |
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-1:000000000000 | 0:915e5c5e02e6 |
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1 <?xml version="1.0"?> | |
2 <tool id="filter_bed_on_splice_junctions" name="Filter BED on splice junctions" version="0.0.1"> | |
3 <description>that are not in a reference bed file</description> | |
4 <command interpreter="python">filter_bed_on_splice_junctions.py --input "$input_bed" | |
5 --guided_junctions "$guided_junctions" | |
6 #if $leading_bp: | |
7 --leading_bp $leading_bp | |
8 #end if | |
9 #if $trailing_bp: | |
10 --trailing_bp $trailing_bp | |
11 #end if | |
12 --novel_junctions "$novel_junctions" | |
13 </command> | |
14 <inputs> | |
15 <param name="input_bed" type="data" format="bed" label="BED file" | |
16 help="e.g. tophat junctions.bed run without GTF option or no-novel-junctions"/> | |
17 <param name="guided_junctions" type="data" format="bed" optional="true" label="reference bed file" | |
18 help="e.g. tophat junctions.bed run with GTF option and no-novel-junctions"/> | |
19 <param name="leading_bp" type="integer" value="" min="0" optional="true" label="Extend the start position" | |
20 help="The number of base pairs to extend the start of the exon before the junction position"/> | |
21 <param name="trailing_bp" type="integer" value="" min="0" optional="true" label="Extend the end position" | |
22 help="The number of base pairs to extend the end of the exon after the junction position"/> | |
23 </inputs> | |
24 <stdio> | |
25 <exit_code range="1:" level="fatal" description="Error" /> | |
26 </stdio> | |
27 <outputs> | |
28 <data name="novel_junctions" metadata_source="input_bed" format="bed"/> | |
29 </outputs> | |
30 <tests> | |
31 <test> | |
32 <param name="input_bed" value="novel_splice_junctions.bed" ftype="bed" dbkey="hg19"/> | |
33 <param name="guided_junctions" value="gtf_splice_junctions.bed" ftype="bed" dbkey="hg19"/> | |
34 <param name="leading_bp" value="0"/> | |
35 <param name="trailing_bp" value="0"/> | |
36 <output name="novel_junctions" file="filtered_novel_splice_junctions.bed"/> | |
37 </test> | |
38 <test> | |
39 <param name="input_bed" value="novel_splice_junctions.bed" ftype="bed" dbkey="hg19"/> | |
40 <param name="guided_junctions" value="gtf_splice_junctions.bed" ftype="bed" dbkey="hg19"/> | |
41 <param name="leading_bp" value="10"/> | |
42 <param name="trailing_bp" value="10"/> | |
43 <output name="novel_junctions" file="extended_novel_splice_junctions.bed"/> | |
44 </test> | |
45 </tests> | |
46 <help> | |
47 **Filter BED on splice junctions** | |
48 | |
49 Filter out lines of a BED file that have junctions that are in in the reference bed file of known junctions. | |
50 The start position of the exon preceding the junction and the end position of the exon after the junction can be extended. | |
51 This is to compensate for alignments that may not include enough of the exons surrounding the junctions. | |
52 | |
53 A typical application would be to run tophat twice, | |
54 once with the --GTF and --no-novel-juncs options for well known splice junctions, | |
55 then a second time without those options to also include novel splice junctions. | |
56 | |
57 This application would filter out the well splice known junctions | |
58 from the run intended to find all splice junctions including novel ones. | |
59 | |
60 </help> | |
61 </tool> |