Mercurial > repos > xuebing > sharplabtool
view tools/new_operations/cluster.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="gops_cluster_1" name="Cluster"> <description>the intervals of a dataset</description> <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> <inputs> <param format="interval" name="input1" type="data"> <label>Cluster intervals of</label> </param> <param name="distance" size="5" type="integer" value="1" help="(bp)"> <label>max distance between intervals</label> </param> <param name="minregions" size="5" type="integer" value="2"> <label>min number of intervals per cluster</label> </param> <param name="returntype" type="select" label="Return type"> <option value="1">Merge clusters into single intervals</option> <option value="2">Find cluster intervals; preserve comments and order</option> <option value="3">Find cluster intervals; output grouped by clusters</option> <option value="4">Find the smallest interval in each cluster</option> <option value="5">Find the largest interval in each cluster</option> </param> </inputs> <outputs> <data format="input" name="output" metadata_source="input1" /> </outputs> <code file="operation_filter.py"> <hook exec_after_process="exec_after_cluster" /> </code> <tests> <test> <param name="input1" value="5.bed" /> <param name="distance" value="1" /> <param name="minregions" value="2" /> <param name="returntype" value="1" /> <output name="output" file="gops-cluster-1.bed" /> </test> <test> <param name="input1" value="gops_cluster_bigint.bed" /> <param name="distance" value="1" /> <param name="minregions" value="2" /> <param name="returntype" value="1" /> <output name="output" file="gops-cluster-1.bed" /> </test> <test> <param name="input1" value="5.bed" /> <param name="distance" value="1" /> <param name="minregions" value="2" /> <param name="returntype" value="2" /> <output name="output" file="gops-cluster-2.bed" /> </test> <test> <param name="input1" value="5.bed" /> <param name="distance" value="1" /> <param name="minregions" value="2" /> <param name="returntype" value="3" /> <output name="output" file="gops-cluster-3.bed" /> </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. ----- **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 ----- **Syntax** - **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. - **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. - **Merge clusters into single intervals** outputs intervals that span the entire cluster. - **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file. - **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. ----- **Example** .. image:: ./static/operation_icons/gops_cluster.gif </help> </tool>