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97 lines
3.9 KiB
XML
97 lines
3.9 KiB
XML
<tool id="gops_cluster_1" name="Cluster">
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<description>the intervals of a dataset</description>
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<trackster_conf/>
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<command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command>
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<inputs>
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<param format="interval" name="input1" type="data">
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<label>Cluster intervals of</label>
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</param>
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<param name="distance" size="5" type="integer" value="1" help="(bp)">
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<label>max distance between intervals</label>
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</param>
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<param name="minregions" size="5" type="integer" value="2">
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<label>min number of intervals per cluster</label>
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</param>
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<param name="returntype" type="select" label="Return type">
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<option value="1">Merge clusters into single intervals</option>
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<option value="2">Find cluster intervals; preserve comments and order</option>
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<option value="3">Find cluster intervals; output grouped by clusters</option>
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<option value="4">Find the smallest interval in each cluster</option>
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<option value="5">Find the largest interval in each cluster</option>
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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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<hook exec_after_process="exec_after_cluster" />
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</code>
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<tests>
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<test>
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<param name="input1" value="5.bed" />
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<param name="distance" value="1" />
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<param name="minregions" value="2" />
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<param name="returntype" value="1" />
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<output name="output" file="gops-cluster-1.bed" />
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</test>
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<test>
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<param name="input1" value="gops_cluster_bigint.bed" />
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<param name="distance" value="1" />
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<param name="minregions" value="2" />
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<param name="returntype" value="1" />
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<output name="output" file="gops-cluster-1.bed" />
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</test>
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<test>
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<param name="input1" value="5.bed" />
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<param name="distance" value="1" />
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<param name="minregions" value="2" />
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<param name="returntype" value="2" />
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<output name="output" file="gops-cluster-2.bed" />
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</test>
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<test>
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<param name="input1" value="5.bed" />
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<param name="distance" value="1" />
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<param name="minregions" value="2" />
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<param name="returntype" value="3" />
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<output name="output" file="gops-cluster-3.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 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.
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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://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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**Syntax**
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- **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered "clustered". **Negative** values for distance are allowed, and are useful for clustering intervals that overlap.
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- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster. Any area with less than this minimum will not be included in the output.
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- **Merge clusters into single intervals** outputs intervals that span the entire cluster.
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- **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file.
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- **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost.
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-----
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**Examples**
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Find Clusters:
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.. image:: ${static_path}/operation_icons/gops_clusterFind.gif
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Merge Clusters:
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.. image:: ${static_path}/operation_icons/gops_clusterMerge.gif
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</help>
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</tool>
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