annotate metaintv.xml @ 11:b7f1d9f8f3bc

Uploaded
author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
1 <tool id="metaintv" name="binned-average">
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
2 <description>from bigwig</description>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python">binnedAverage.py $bwfile $intvfile $nbin $outfile $outplot </command>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
4 <inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
5 <param name="intvfile" format="bed" type="data" label="BED file (require strand in column 6)"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
6 <param name="bwfile" format="bigwig" type="data" label="BigWig file"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
7 <param name="nbin" type="integer" value="20" label="number of bins"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
8
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
9 </inputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
10 <outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
11 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}[data]"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
12 <data format="pdf" name="outplot" label="${tool.name} on ${on_string}[plot]"/>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
13 </outputs>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
14 <help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
15
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
16 .. class:: infomark
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
17
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
18 Each interval is binned and the average base-resolution score/coverage/density in the bigwig file is added as new columns appended at the end of the original file .
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
19
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
20 **Example**
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
21
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
22 If your original data has the following format:
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
23
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
24 +-----+-----+---+------+
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
25 |chrom|start|end|other2|
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
26 +-----+-----+---+------+
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
27
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
28 and you choose to divide each interval into 3 bins and return the mean scores of each bin, your output will look like this:
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
29
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
30 +-----+-----+---+------+-----+-----+-----+
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
31 |chrom|start|end|other2|mean1|mean2|mean3|
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
32 +-----+-----+---+------+-----+-----+-----+
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
33
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
34
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
35 </help>
b7f1d9f8f3bc Uploaded
xuebing
parents:
diff changeset
36 </tool>