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Daniel Blankenberg
86f0862aa4
Cron scripts on test and main will need to be updated when the server is. GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
56 lines
1.8 KiB
XML
56 lines
1.8 KiB
XML
<tool id="gops_complement_1" name="Complement">
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<description>intervals of a query</description>
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<command interpreter="python">gops_complement.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len $allchroms</command>
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<inputs>
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<param format="interval" name="input1" type="data">
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<label>Complement regions of</label>
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</param>
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<param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
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</param>
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</inputs>
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<outputs>
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<data format="input" name="output" metadata_source="input1" />
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</outputs>
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<code file="operation_filter.py"/>
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<tests>
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<test>
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<param name="input1" value="1.bed" />
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<param name="allchroms" value="true" />
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<output name="output" file="gops_complement_out.bed" />
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</test>
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<test>
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<param name="input1" value="gops_bigint.interval" />
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<param name="allchroms" value="true" />
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<output name="output" file="gops_complement_out2.bed" />
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</test>
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</tests>
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<help>
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.. class:: infomark
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**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns
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This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval.
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-----
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**Screencasts!**
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/GopsDesc
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-----
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**Syntax**
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- **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the query.
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-----
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**Example**
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.. image:: ../static/operation_icons/gops_complement.gif
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</help>
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</tool> |