|
1
|
1 <tool id="jamm" name="JAMM" version="1.0.7">
|
|
0
|
2 <description>Calls peaks on NGS data</description>
|
|
|
3 <requirements>
|
|
1
|
4 <requirement>R</requirement>
|
|
|
5 <requirement>perl</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command interpreter="python">
|
|
1
|
8 <![CDATA[
|
|
|
9 jammwrapper.py -i
|
|
|
10 #for $x in $input
|
|
|
11 ${x.replicate.file_name} #end for
|
|
|
12
|
|
|
13 #for $x in $control
|
|
|
14 -c ${x.controlreplicate.file_name} #end for
|
|
|
15
|
|
|
16 -g ${genomeSizeFile}
|
|
|
17 -o $output
|
|
|
18 -of $outputfiltered
|
|
0
|
19 -m $mode
|
|
|
20 -r $resolution
|
|
1
|
21 -p $processes
|
|
|
22 -t $type
|
|
|
23 -f $fraglen
|
|
|
24 -b $binsize
|
|
|
25 ]]>
|
|
0
|
26 </command>
|
|
|
27
|
|
|
28 <stdio>
|
|
|
29 <!-- Wrapper ensures anything other than zero is an error -->
|
|
|
30 <exit_code range="1:" />
|
|
|
31 <exit_code range=":-1" />
|
|
|
32 </stdio>
|
|
|
33
|
|
|
34 <inputs>
|
|
1
|
35 <repeat name="input" title="Sample Replicates">
|
|
|
36 <param name="replicate" type="data" format="bed"></param>
|
|
|
37 </repeat>
|
|
|
38
|
|
|
39 <repeat name="control" title="Negative Control Replicates (e.g. input) - optional">
|
|
|
40 <param name="controlreplicate" type="data" format="bed"></param>
|
|
|
41 </repeat>
|
|
|
42
|
|
|
43 <param name="genomeSizeFile" type="data" label="File indicating chromosome sizes" description="Chromosome size"></param>
|
|
0
|
44 <param name="mode" type="select" label="Mode (normal or narrow)">
|
|
|
45 <option value="normal">normal</option>
|
|
|
46 <option value="narrow">narrow</option>
|
|
|
47 </param>
|
|
|
48 <param name="resolution" type="select" label="Resolution (peak or region)">
|
|
|
49 <option value="peak">peak</option>
|
|
|
50 <option value="region">region</option>
|
|
1
|
51 <option value="window">window</option>
|
|
0
|
52 </param>
|
|
1
|
53 <param name="type" type="select" label="Type of data (Single or paired. Paired requires BEDPE datasets)">
|
|
|
54 <option value="single" selected="true">single</option>
|
|
|
55 <option value="paired">paired</option>
|
|
|
56 </param>
|
|
|
57 <param name="fraglen" type="text" value="ns" label="Fragment length. Estimated by default (ns)" />
|
|
|
58 <param name="binsize" type="text" value="ns" label="Bin size. Estimated by default (ns)" />
|
|
|
59 <param name="processes" type="text" value="4" label="Number of threads used by R" help="Depending on your Galaxy configuration, 1 should be safe and up to 4 should be fine." />
|
|
|
60
|
|
0
|
61 </inputs>
|
|
|
62
|
|
|
63 <outputs>
|
|
|
64 <data name="output" format="tabular" label="Narrowpeak tabular" />
|
|
1
|
65 <data name="outputfiltered" format="tabular" label="Narrowpeak tabular filtered" />
|
|
0
|
66 </outputs>
|
|
|
67
|
|
|
68 <tests>
|
|
|
69 <test>
|
|
1
|
70 <param name="replicate" value="test1.bed" ftype="bed"/>
|
|
|
71 <param name="replicate" value="test2.bed" ftype="bed"/>
|
|
0
|
72 <param name="genomeSizeFile" value="chrSizes21.csize"/>
|
|
|
73 <output name="output" ftype="tabular">
|
|
|
74 <assert_contents>
|
|
|
75 <has_text text="chr21" />
|
|
|
76 </assert_contents>
|
|
|
77 </output>
|
|
|
78 </test>
|
|
1
|
79 <test>
|
|
|
80 <param name="replicate" value="test1.bed" ftype="bed"/>
|
|
|
81 <param name="replicate" value="test2.bed" ftype="bed"/>
|
|
|
82 <param name="controlreplicate" value="control.bed" />
|
|
|
83 <param name="genomeSizeFile" value="chrSizes21.csize"/>
|
|
|
84 <param name="resolution" value="region" />
|
|
|
85 <output name="output" ftype="tabular">
|
|
|
86 <assert_contents>
|
|
|
87 <has_text text="chr21" />
|
|
|
88 </assert_contents>
|
|
|
89 </output>
|
|
|
90 </test>
|
|
0
|
91 </tests>
|
|
|
92
|
|
|
93 <citations>
|
|
|
94 <!-- Example of annotating a citation using a DOI. -->
|
|
|
95 <citation type="doi">10.1093/bioinformatics/btu568</citation>
|
|
|
96 </citations>
|
|
|
97 <help>
|
|
1
|
98 **What it does**
|
|
|
99 JAMM calls peaks on NGS data, i.e. for finding binding sites.
|
|
|
100
|
|
|
101 .. class:: warningmark
|
|
0
|
102
|
|
|
103 This tool requires files in *bed* format.
|
|
|
104
|
|
1
|
105 .. class:: infomark
|
|
|
106
|
|
|
107 If you are just starting out, you can find some sensible parameter choices here:
|
|
|
108
|
|
|
109 http://code.google.com/p/jamm-peak-finder/wiki/Usage#Examples
|
|
0
|
110
|
|
1
|
111 * ChIP-Seq TF: everything default
|
|
|
112 * ChIP-Seq HM: Binsize=200
|
|
|
113 * ChIP-Seq Broad HM: Binsize=200 Resolution=region
|
|
|
114 * ChIP-Seq Very Broad HM: Binsize=10000 Resolution=window
|
|
|
115 * DNase-seq: Fragment length=1
|
|
0
|
116 </help>
|
|
|
117 </tool>
|
