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author greg
date Thu, 10 Mar 2016 10:34:37 -0500
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1 <tool id="paired_end_cross_plot" name="Paired-end cross plot" version="1.0.0">
2 <description></description>
3 <command>
4 <![CDATA[
5 java -jar $__tool_directory__/pairedendCrossPlot.jar
6 -f "$input1"
7 -r "$input2"
8 -w $window_size
9 -o "$output" 1>/dev/null
10 ]]>
11 </command>
12 <inputs>
13 <param name="input1" type="data" format="scidx" label="Read 1 ScIdx file" />
14 <param name="input2" type="data" format="scidx" label="Read 2 ScIdx file" />
15 <param name="window_size" type="integer" value="500" min="1" label="Size of window upstream and downstream around the reference point in base pairs" />
16 </inputs>
17 <outputs>
18 <data name="output" format="tabular" />
19 </outputs>
20 <tests>
21 <test>
22 <param name="input1" value="input1.scidx" ftype="scidx"/>
23 <param name="input2" value="input2.scidx" ftype="scidx"/>
24 <param name="window_size" value="500"/>
25 <output name="output" file="output1.tabular" ftype="tabular"/>
26 </test>
27 <test>
28 <param name="input1" value="input3.scidx" ftype="scidx"/>
29 <param name="input2" value="input4.scidx" ftype="scidx"/>
30 <param name="window_size" value="500"/>
31 <output name="output" file="output2.tabular" ftype="tabular"/>
32 </test>
33 </tests>
34 <help>
35
36 **What it does**
37
38 Produces a frequency histogram of the relative occurrence of Read2 5' ends relative to the
39 start of every Read1 5' end in a user-specified coordinate window.
40
41 -----
42
43 **Options**
44
45 * **Window Size** - sets the size of the window upstream and downstream around the reference point in base pairs.
46
47 </help>
48 <citations>
49 <citation type="bibtex">
50 @unpublished{None,
51 author = {Lai, William},
52 title = {None},
53 year = {None},
54 eprint = {None},
55 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
56 }</citation>
57 </citations>
58 </tool>