/tools/new_operations/basecoverage.xml

 1<tool id="gops_basecoverage_1" name="Base Coverage">
 2  <description>of all intervals</description>
 3  <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
 4  <inputs>
 5    <param format="interval" name="input1" type="data">
 6      <label>Compute coverage for</label>
 7    </param>
 8   </inputs>
 9  <outputs>
10    <data format="txt" name="output" />
11  </outputs>
12  <code file="operation_filter.py"/>
13  <tests>
14    <test>
15      <param name="input1" value="1.bed" />
16      <output name="output" file="gops_basecoverage_out.txt" />     
17    </test>
18    <test>
19      <param name="input1" value="gops_bigint.interval" />
20      <output name="output" file="gops_basecoverage_out2.txt" />     
21    </test>
22  </tests>
23  <help>
24
25.. class:: infomark
26
27**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
28
29This operation counts the total bases covered by a set of intervals.  Bases that are covered by more than one interval are **not** counted more than once towards the total.
30
31-----
32
33**Screencasts!**
34
35See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
36
37.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
38
39**Example**
40
41.. image:: ${static_path}/operation_icons/gops_baseCoverage.gif
42
43
44</help>
45</tool>