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1 <tool id="gops_cluster_1" name="Cluster" version="0.0.1">
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2 <description>the intervals of a dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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7 <trackster_conf/>
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8 <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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9 <inputs>
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10 <param format="interval" name="input1" type="data">
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11 <label>Cluster intervals of</label>
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12 </param>
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13 <param name="distance" size="5" type="integer" value="1" help="(bp)">
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14 <label>max distance between intervals</label>
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15 </param>
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16 <param name="minregions" size="5" type="integer" value="2">
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17 <label>min number of intervals per cluster</label>
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18 </param>
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19 <param name="returntype" type="select" label="Return type">
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20 <option value="1">Merge clusters into single intervals</option>
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21 <option value="2">Find cluster intervals; preserve comments and order</option>
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22 <option value="3">Find cluster intervals; output grouped by clusters</option>
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23 <option value="4">Find the smallest interval in each cluster</option>
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24 <option value="5">Find the largest interval in each cluster</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format="input" name="output" metadata_source="input1" />
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29 </outputs>
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30 <code file="operation_filter.py">
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31 <hook exec_after_process="exec_after_cluster" />
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32 </code>
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33 <tests>
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34 <test>
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35 <param name="input1" value="5.bed" />
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36 <param name="distance" value="1" />
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37 <param name="minregions" value="2" />
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38 <param name="returntype" value="1" />
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39 <output name="output" file="gops-cluster-1.bed" />
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40 </test>
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41 <test>
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42 <param name="input1" value="gops_cluster_bigint.bed" />
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43 <param name="distance" value="1" />
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44 <param name="minregions" value="2" />
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45 <param name="returntype" value="1" />
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46 <output name="output" file="gops-cluster-1.bed" />
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47 </test>
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48 <test>
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49 <param name="input1" value="5.bed" />
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50 <param name="distance" value="1" />
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51 <param name="minregions" value="2" />
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52 <param name="returntype" value="2" />
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53 <output name="output" file="gops-cluster-2.bed" />
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54 </test>
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55 <test>
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56 <param name="input1" value="5.bed" />
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57 <param name="distance" value="1" />
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58 <param name="minregions" value="2" />
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59 <param name="returntype" value="3" />
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60 <output name="output" file="gops-cluster-3.bed" />
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61 </test>
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62 </tests>
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63 <help>
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64
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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 -----
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70
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71 **Screencasts!**
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72
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73 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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74
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75 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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76
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77 -----
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78
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79 **Syntax**
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80
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81 - **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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82 - **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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83 - **Merge clusters into single intervals** outputs intervals that span the entire cluster.
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84 - **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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85 - **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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86
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87 -----
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88
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89 **Examples**
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90
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91 Find Clusters:
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92
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93 .. image:: ${static_path}/operation_icons/gops_clusterFind.gif
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94
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95 Merge Clusters:
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96
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97 .. image:: ${static_path}/operation_icons/gops_clusterMerge.gif
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98
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99 </help>
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100 </tool>
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