|
6
|
1 <tool id="rm_spurious_events.py" name="Remove spurious" version="0.1.0">
|
|
|
2 <description>crosslinking events</description>
|
|
56
|
3 <requirements>
|
|
|
4 <requirement type="package" version="8.22">gnu_coreutils</requirement>
|
|
|
5 <requirement type="package" version="5.18.1">perl</requirement>
|
|
|
6 </requirements>
|
|
0
|
7 <macros>
|
|
|
8 <import>macros.xml</import>
|
|
|
9 </macros>
|
|
|
10 <expand macro="stdio" />
|
|
50
|
11 <version_command>python $__tool_directory__/rm_spurious_events.py --version</version_command>
|
|
0
|
12 <command interpreter="python"><![CDATA[rm_spurious_events.py
|
|
|
13 #if $positional_1 and $positional_1 is not None:
|
|
|
14 $positional_1
|
|
|
15 #end if
|
|
|
16
|
|
|
17 #if $threshold and $threshold is not None:
|
|
|
18 --threshold $threshold
|
|
|
19 #end if
|
|
50
|
20 --outfile $default]]></command>
|
|
0
|
21 <inputs>
|
|
|
22 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
|
|
|
23 <param help="(--threshold)" label="Threshold for spurious event removal." name="threshold" optional="true" type="float" value="0.1"/>
|
|
|
24 </inputs>
|
|
|
25 <outputs>
|
|
|
26 <data format="bed" hidden="false" name="default"/>
|
|
|
27 </outputs>
|
|
|
28 <tests>
|
|
|
29 <test>
|
|
|
30 <param name="positional_1" value="merged_pcr_dupes_spurious.bed"/>
|
|
|
31 <param name="threshold" value="0.5"/>
|
|
|
32 <output name="default" file="merged_pcr_dupes_spurious_filtered_thresh05.bed"/>
|
|
|
33 </test>
|
|
|
34 </tests>
|
|
|
35 <help><![CDATA[
|
|
|
36 Remove spurious events originating from errors in random sequence tags.
|
|
|
37
|
|
6
|
38 This tool compares all events sharing the same coordinates. Among each group
|
|
0
|
39 of events the maximum number of PCR duplicates is determined. All events that
|
|
|
40 are supported by less than 10 percent of this maximum count are removed.
|
|
|
41
|
|
6
|
42 Input::
|
|
|
43
|
|
|
44 * bed6 file containing crosslinking events with score field set to number of PCR duplicates
|
|
0
|
45
|
|
6
|
46 Output::
|
|
|
47
|
|
|
48 * bed6 file with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand
|
|
0
|
49
|
|
|
50 Author: Daniel Maticzka
|
|
|
51 Copyright: 2015
|
|
|
52 License: Apache
|
|
|
53 Email: maticzkd@informatik.uni-freiburg.de
|
|
|
54 Status: Testing
|
|
|
55 ]]></help>
|
|
|
56 <expand macro="citations" />
|
|
|
57 </tool>
|
