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annotate intersect.xml @ 5:60925436ca5f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:50:20 -0400
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60925436ca5f 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">
60925436ca5f 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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devteam
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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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devteam
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8 <command><![CDATA[
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9 python '$__tool_directory__/gops_intersect.py'
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10 '$input1'
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11 '$input2'
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12 '$output'
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13
60925436ca5f 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')
60925436ca5f 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
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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16 #else:
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17 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
60925436ca5f 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
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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19
60925436ca5f 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')
60925436ca5f 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
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 #else:
60925436ca5f 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}
60925436ca5f 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
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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25
60925436ca5f 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
60925436ca5f 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)">
60925436ca5f 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>
60925436ca5f 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" />
60925436ca5f 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" />
60925436ca5f 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)" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 </inputs>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 <outputs>
60925436ca5f 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"/>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 </outputs>
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40 <tests>
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41 <test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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42 <param name="input1" value="1.bed" />
60925436ca5f 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" />
60925436ca5f 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" />
60925436ca5f 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="" />
60925436ca5f 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" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 </test>
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48 <test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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49 <param name="input1" value="1.bed" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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50 <param name="input2" value="2_mod.bed" ftype="interval"/>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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51 <param name="min" value="1" />
60925436ca5f 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="" />
60925436ca5f 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" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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54 </test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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55 <test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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56 <param name="input1" value="1.bed" />
60925436ca5f 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"/>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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58 <param name="min" value="1" />
60925436ca5f 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" />
60925436ca5f 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" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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61 </test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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62 <test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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63 <param name="input1" value="1.bed" />
60925436ca5f 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" />
60925436ca5f 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" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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66 <param name="returntype" value="Overlapping pieces of Intervals" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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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" />
60925436ca5f 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" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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72 <param name="min" value="1" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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73 <param name="returntype" value="" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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74 <output name="output" file="gops_intersect_bigint_out.interval" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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75 </test>
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76 <test>
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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77 <param name="input1" value="gops_bigint2.interval" ftype="interval" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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78 <param name="input2" value="gops_bigint.interval" ftype="interval" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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79 <param name="min" value="1" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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80 <param name="returntype" value="" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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81 <output name="output" file="gops_intersect_bigint_out.interval" />
60925436ca5f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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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>