annotate intersect.xml @ 6:69c10b56f46d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9
author devteam
date Mon, 13 Jun 2022 16:23:33 +0000
parents 33b3f3688db4
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33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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1 <tool id="gops_intersect_1" name="Intersect" version="1.0.0">
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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2 <description>the intervals of two datasets</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"/>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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8 <command><![CDATA[
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9 python '$__tool_directory__/gops_intersect.py'
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10 '$input1'
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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11 '$input2'
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12 '$output'
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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13
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 #if $input1.is_of_type('gff')
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 -1 1,4,5,7 --gff1
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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16 #else:
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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17 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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18 #end if
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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19
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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20 #if $input2.is_of_type('gff')
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 -2 1,4,5,7 --gff2
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 #else:
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 #end if
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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25
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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26 -m $min $returntype
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 ]]></command>
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28 <inputs>
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29 <param name="returntype" type="select" label="Return" help="(see figure below)">
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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30 <option value="">Overlapping Intervals</option>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 <option value="-p">Overlapping pieces of Intervals</option>
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32 </param>
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33 <param name="input1" type="data" format="interval,gff" label="of" help="First dataset" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 <param name="input2" type="data" format="interval,gff" label="that intersect" help="Second dataset" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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35 <param name="min" type="integer" value="1" min="1" label="for at least" help="(bp)" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 </inputs>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 <outputs>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 <data name="output" format_source="input1" metadata_source="input1"/>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 </outputs>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 <tests>
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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41 <test>
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42 <param name="input1" value="1.bed" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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43 <param name="input2" value="2.bed" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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44 <param name="min" value="1" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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45 <param name="returntype" value="" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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46 <output name="output" file="gops_intersect_out.bed" />
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47 </test>
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48 <test>
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49 <param name="input1" value="1.bed" />
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50 <param name="input2" value="2_mod.bed" ftype="interval"/>
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51 <param name="min" value="1" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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52 <param name="returntype" value="" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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53 <output name="output" file="gops_intersect_diffCols.bed" />
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54 </test>
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55 <test>
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56 <param name="input1" value="1.bed" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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57 <param name="input2" value="2_mod.bed" ftype="interval"/>
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58 <param name="min" value="1" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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59 <param name="returntype" value="Overlapping pieces of Intervals" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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60 <output name="output" file="gops_intersect_p_diffCols.bed" />
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61 </test>
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62 <test>
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63 <param name="input1" value="1.bed" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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64 <param name="input2" value="2.bed" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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65 <param name="min" value="10" />
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66 <param name="returntype" value="Overlapping pieces of Intervals" />
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67 <output name="output" file="gops_intersect_p_out.bed" />
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68 </test>
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69 <test>
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70 <param name="input1" value="gops_bigint.interval" ftype="interval" />
33b3f3688db4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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71 <param name="input2" value="gops_bigint2.interval" ftype="interval" />
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72 <param name="min" value="1" />
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73 <param name="returntype" value="" />
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74 <output name="output" file="gops_intersect_bigint_out.interval" />
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75 </test>
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76 <test>
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77 <param name="input1" value="gops_bigint2.interval" ftype="interval" />
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78 <param name="input2" value="gops_bigint.interval" ftype="interval" />
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79 <param name="min" value="1" />
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80 <param name="returntype" value="" />
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81 <output name="output" file="gops_intersect_bigint_out.interval" />
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82 </test>
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83 <test>
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84 <param name="input1" value="12.bed" ftype="bed" />
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85 <param name="input2" value="1.bed" ftype="bed" />
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86 <param name="min" value="1" />
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87 <param name="returntype" value="" />
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88 <output name="output" file="gops_intersect_no_strand_out.bed" />
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89 </test>
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90 <!-- Intersect two GFF files. -->
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91 <test>
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92 <param name="input1" value="gops_subtract_in1.gff" />
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93 <param name="input2" value="gops_subtract_in2.gff" />
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94 <param name="min" value="1" />
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95 <param name="returntype" value="" />
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96 <output name="output" file="gops_intersect_out2.gff" />
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97 </test>
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98 <!-- Intersect GFF file and bed file. -->
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99 <test>
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100 <param name="input1" value="gops_subtract_in1.gff" />
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101 <param name="input2" value="gops_subtract_in2.bed" />
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102 <param name="min" value="1" />
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103 <param name="returntype" value="" />
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104 <output name="output" file="gops_intersect_out2.gff" />
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 .. class:: infomark
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109
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110 **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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111
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112 @SCREENCASTS@
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113
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114 **Syntax**
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115
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116 - **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two datasets
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117 - **Overlapping Intervals** returns entire intervals from the first dataset that overlap the second dataset. The returned intervals are completely unchanged, and this option only filters out intervals that do not overlap with the second dataset.
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118 - **Overlapping pieces of Intervals** returns intervals that indicate the exact base pair overlap between the first dataset and the second dataset. The intervals returned are from the first dataset, and all fields besides start and end are guaranteed to remain unchanged.
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119
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120 -----
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121
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122 **Examples**
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123
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124 Overlapping Intervals:
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125
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126 .. image:: gops_intersectOverlappingIntervals.gif
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127
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128 Overlapping Pieces of Intervals:
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129
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130 .. image:: gops_intersectOverlappingPieces.gif
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131 ]]></help>
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132 </tool>