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/tools/liftover/standardize_wig.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 70 lines | 59 code | 11 blank | 0 comment | 0 complexity | 11a4b2ba284cbd2ba28cd7e7fbb4da08 MD5 | raw file
 1<tool name="Standardize wig file" id="filter_std_wig">
 2  <description>Standardize a wig file to a given span</description>
 3  <command interpreter="command">/bin/bash $shscript</command>
 4  <inputs>
 5    <param ftype="wig" format="wig" name="wfile" type="data" label="WIGGLE file"/>
 6    <param name="span" type="select" label="Span">
 7        <option value="8">8</option>
 8        <option value="32">32</option>
 9        <option value="64">64</option>
10        <option value="128">128</option>
11    </param>
12  </inputs>
13  <outputs>
14    <data format="wig" name="output" />
15  </outputs>
16  <configfiles>
17    <configfile name="shscript">
18#!/bin/bash
19
20#set $dollar = chr(36)
21#set $gt = chr(62)
22#set $lt = chr(60)
23#set $ad = chr(38)
24
25standardize_wig.py $wfile $span $output ${ad}${gt}/dev/null
26    
27   </configfile>
28  </configfiles>
29<tests>
30    <test maxseconds="3600" name="StandardizeWig_4">
31    <param name="wfile" value="wiggle.wig" />
32    <param name="span" value="128" />
33    <output name="output" file="standardizewig_4/standardizewig_4.wig" />
34  </test>
35    <test maxseconds="3600" name="StandardizeWig_3">
36    <param name="wfile" value="wiggle.wig" />
37    <param name="span" value="64" />
38    <output name="output" file="standardizewig_3/standardizewig_3.wig" />
39  </test>
40    <test maxseconds="3600" name="StandardizeWig_2">
41    <param name="wfile" value="wiggle.wig" />
42    <param name="span" value="32" />
43    <output name="output" file="standardizewig_2/standardizewig_2.wig" />
44  </test>
45  <test maxseconds="3600" name="StandardizeWig_1">
46    <param name="wfile" value="wiggle.wig" />
47    <param name="span" value="8" />
48    <output name="output" file="standardizewig_1/standardizewig_1.wig" />
49  </test>
50</tests>
51  <help>
52This tool converts a given wig file to conform to a given span. The
53code is written by Jacqueline Wentz.
54
55-----
56
57**Parameters**
58
59- **WIGGLE file** is selected from current history.
60- **Span** is the final resolution in the converted WIGGLE file.
61
62-----
63
64**Output**
65
66- **WIGGLE file** is the converted file.
67
68  </help>
69
70</tool>