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https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Ian Schenck
feda672ffa
- Indexing for tracks done in background with a visual treatment done to Trackster - DB builds can be uploaded by a user (chromInfo/len extension). - TODO: Add ability to change the dbkey of a dataset to any arbitrary string value.
62 lines
2.0 KiB
XML
62 lines
2.0 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 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $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="2_mod.bed" ftype="interval"/>
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<param name="allchroms" value="true" />
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<output name="output" file="gops_complement_out_diffCols.dat" />
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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>
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