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annotate cluster.xml @ 5:2108e2dc3d32 draft default tip

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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 18:38:08 -0400
parents 1e895b74f29f
children
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1
5167eb4b30ca Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_cluster_1" name="Cluster" version="1.0.0">
5
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2 <description>the intervals of a dataset</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <code file="operation_filter.py">
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8 <hook exec_after_process="exec_after_cluster" />
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9 </code>
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10 <command><![CDATA[
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11 python '$__tool_directory__/gops_cluster.py'
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12 '$input1'
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13 '$output'
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14 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 -d $distance
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16 -m $minregions
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17 -o $returntype
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18 ]]></command>
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19 <inputs>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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20 <param name="input1" type="data" format="interval" label="Cluster intervals of" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 <param name="distance" type="integer" value="1" label="Max distance between intervals" help="(bp)" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 <param name="minregions" type="integer" value="2" label="Min number of intervals per cluster" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 <param name="returntype" type="select" label="Return type">
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 <option value="1">Merge clusters into single intervals</option>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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25 <option value="2">Find cluster intervals; preserve comments and order</option>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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26 <option value="3">Find cluster intervals; output grouped by clusters</option>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 <option value="4">Find the smallest interval in each cluster</option>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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28 <option value="5">Find the largest interval in each cluster</option>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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29 </param>
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30 </inputs>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 <outputs>
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32 <data name="output" format_source="input1" metadata_source="input1" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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33 </outputs>
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34 <tests>
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35 <test>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 <param name="input1" value="5.bed" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 <param name="distance" value="1" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 <param name="minregions" value="2" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 <param name="returntype" value="1" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 <output name="output" file="gops-cluster-1.bed" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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41 </test>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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42 <test>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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43 <param name="input1" value="gops_cluster_bigint.bed" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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44 <param name="distance" value="1" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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45 <param name="minregions" value="2" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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46 <param name="returntype" value="1" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 <output name="output" file="gops-cluster-1.bed" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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48 </test>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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49 <test>
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50 <param name="input1" value="5.bed" />
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51 <param name="distance" value="1" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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52 <param name="minregions" value="2" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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53 <param name="returntype" value="2" />
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54 <output name="output" file="gops-cluster-2.bed" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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55 </test>
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56 <test>
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57 <param name="input1" value="5.bed" />
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58 <param name="distance" value="1" />
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59 <param name="minregions" value="2" />
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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60 <param name="returntype" value="3" />
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61 <output name="output" file="gops-cluster-3.bed" />
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62 </test>
2108e2dc3d32 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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63 </tests>
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64 <help><![CDATA[
0
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65 .. class:: infomark
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66
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67 **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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68
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69 @SCREENCASTS@
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70
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71 **Syntax**
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72
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73 - **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered &quot;clustered&quot;. **Negative** values for distance are allowed, and are useful for clustering intervals that overlap.
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74 - **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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75 - **Merge clusters into single intervals** outputs intervals that span the entire cluster.
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76 - **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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77 - **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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78
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79 -----
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80
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81 **Examples**
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82
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83 Find Clusters:
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84
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85 .. image:: gops_clusterFind.gif
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86
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87 Merge Clusters:
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88
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89 .. image:: gops_clusterMerge.gif
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90 ]]></help>
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91 </tool>