annotate intersectSig.xml @ 13:292186c14b08

Uploaded
author xuebing
date Sat, 10 Mar 2012 08:17:36 -0500
parents b7f1d9f8f3bc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
1 <tool id="intersectsig" name="test overlap">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
2 <description>of two interval lists</description>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python"> intersectSig.py $fileA $fileB $outfile $outplot $outshuffle $n $genome $fraction $reciprocal </command>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
4 <inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
5 <param name="fileA" type="data" format="interval" label="Return intervals in file A" />
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
6 <param name="fileB" type="data" format="interval" label="that overlap with intervals in file B" />
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
7 <param name="genome" type="select" label="Select genome">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
11 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
12 </param>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
13 <param name="fraction" size="10" type="float" value="1e-9" label="Minimum overlap required as a fraction of interval in file A" help="Default is 1E-9 (i.e., 1bp)."/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
14 <param name="reciprocal" label="Require that the fraction overlap be reciprocal for A and B" type="boolean" truevalue="-r" falsevalue="" checked="False"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
15 <param name="n" size="10" type="integer" value="100" label="Number of permutations to run" help="File A is shuffled this number of times and the number of random overlaps is used to estimate the null distribution and compute the p value"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
16 </inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
17 <outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
18 <data format="interval" name="outfile" label="${tool.name} on ${on_string}:overlap"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
19 <data format="txt" name="outshuffle" label="${tool.name} on ${on_string}:null"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
20 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}:plot"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
21 </outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
22 <help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
23
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
24 **What it does**
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
25
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
26 This tool uses intersectBed to find intervals in the first dataset that overlap with intervals in the second dataset. To estimate the significance of the overlap, the first dataset is shuffled then intersect with the second dataset to generate a null distribution of the number of overlaps. The tool returns venn diagram plot, histogram of the null distribution, overlapped intervals from the first input, and the null distribution of overlaps.
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
27
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
28 </help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
29 </tool>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
30