/tools/new_operations/basecoverage.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 45 lines · 34 code · 11 blank · 0 comment · 0 complexity · a4975e5348e8788e00f6e77a4a7808f2 MD5 · raw file
- <tool id="gops_basecoverage_1" name="Base Coverage">
- <description>of all intervals</description>
- <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
- <inputs>
- <param format="interval" name="input1" type="data">
- <label>Compute coverage for</label>
- </param>
- </inputs>
- <outputs>
- <data format="txt" name="output" />
- </outputs>
- <code file="operation_filter.py"/>
- <tests>
- <test>
- <param name="input1" value="1.bed" />
- <output name="output" file="gops_basecoverage_out.txt" />
- </test>
- <test>
- <param name="input1" value="gops_bigint.interval" />
- <output name="output" file="gops_basecoverage_out2.txt" />
- </test>
- </tests>
- <help>
- .. class:: infomark
- **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.
- This 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.
- -----
- **Screencasts!**
- See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
- .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
- **Example**
- .. image:: ${static_path}/operation_icons/gops_baseCoverage.gif
- </help>
- </tool>