Mercurial > repos > devteam > cluster
diff cluster.xml @ 4:05696474ee89 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
| author | devteam |
|---|---|
| date | Thu, 22 Jun 2017 18:40:19 -0400 |
| parents | 765ceb06c3e2 |
| children |
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--- a/cluster.xml Wed Nov 11 12:47:24 2015 -0500 +++ b/cluster.xml Thu Jun 22 18:40:19 2017 -0400 @@ -1,80 +1,72 @@ <tool id="gops_cluster_1" name="Cluster" version="1.0.0"> - <description>the intervals of a dataset</description> - <requirements> - <requirement type="package" version="0.7.1">bx-python</requirement> - <requirement type="package" version="1.0.0">galaxy-ops</requirement> - </requirements> - <trackster_conf/> - <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" type="integer" value="1" help="(bp)"> - <label>max distance between intervals</label> - </param> - <param name="minregions" 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> - + <description>the intervals of a dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="operation_filter.py"> + <hook exec_after_process="exec_after_cluster" /> + </code> + <command><![CDATA[ +python '$__tool_directory__/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 name="input1" type="data" format="interval" label="Cluster intervals of" /> + <param name="distance" type="integer" value="1" label="Max distance between intervals" help="(bp)" /> + <param name="minregions" type="integer" value="2" label="Min number of intervals per cluster" /> + <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 name="output" format_source="input1" metadata_source="input1" /> + </outputs> + <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><![CDATA[ .. 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 - ------ +@SCREENCASTS@ **Syntax** @@ -95,6 +87,5 @@ Merge Clusters: .. image:: gops_clusterMerge.gif - -</help> + ]]></help> </tool>