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annotate join.xml @ 5:ddf5484243d2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:50:39 -0400
parents 860e7e4899b1
children
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1
4ce471410d01 Corrected version string.
devteam <devteam@galaxyproject.org>
parents: 0
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1 <tool id="gops_join_1" name="Join" version="1.0.0">
5
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2 <description>the intervals of two datasets side-by-side</description>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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3 <macros>
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devteam
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4 <import>macros.xml</import>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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5 </macros>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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6 <expand macro="requirements" />
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7 <code file="operation_filter.py"/>
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8 <command><![CDATA[
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9 python '$__tool_directory__/gops_join.py'
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 '$input1'
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11 '$input2'
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12 '$output'
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13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 -m $min
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16 -f $fill
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17 ]]></command>
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18 <inputs>
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19 <param name="input1" type="data" format="interval" label="Join" help="First dataset" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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20 <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 <param name="min" type="integer" value="1" label="With min overlap" help="(bp)" />
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22 <param name="fill" type="select" label="Return">
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 <option value="none">Only records that are joined (INNER JOIN)</option>
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24 <option value="right">All records of first dataset (fill null with ".")</option>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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25 <option value="left">All records of second dataset (fill null with ".")</option>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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26 <option value="both">All records of both datasets (fill nulls with ".")</option>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data name="output" format_source="input1" metadata_source="input1" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 </outputs>
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32 <tests>
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33 <test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 <param name="input1" value="1.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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35 <param name="input2" value="2.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 <param name="min" value="1" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 <param name="fill" value="none" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 <output name="output" file="gops-join-none.dat" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 </test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 <test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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41 <param name="input1" value="1.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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42 <param name="input2" value="2.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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43 <param name="min" value="1" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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44 <param name="fill" value="right" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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45 <output name="output" file="gops-join-right.dat" />
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46 </test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 <test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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48 <param name="input1" value="1.bed" />
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49 <param name="input2" value="2.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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50 <param name="min" value="1" />
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51 <param name="fill" value="left" />
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52 <output name="output" file="gops-join-left.dat" />
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53 </test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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54 <test>
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55 <param name="input1" value="1.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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56 <param name="input2" value="2.bed" />
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57 <param name="min" value="1" />
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58 <param name="fill" value="both" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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59 <output name="output" file="gops-join-both.dat" />
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60 </test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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61 <test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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62 <param name="input1" value="1.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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63 <param name="input2" value="2.bed" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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64 <param name="min" value="500" />
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65 <param name="fill" value="none" />
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66 <output name="output" file="gops-join-none-500.dat" />
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67 </test>
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68 <test>
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69 <param name="input1" value="1.bed" />
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70 <param name="input2" value="2.bed" />
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71 <param name="min" value="100" />
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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72 <param name="fill" value="both" />
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73 <output name="output" file="gops-join-both-100.dat" />
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74 </test>
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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75 </tests>
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76 <help><![CDATA[
0
cb9ed67cb329 Imported from capsule None
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77 .. class:: infomark
cb9ed67cb329 Imported from capsule None
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78
cb9ed67cb329 Imported from capsule None
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79 **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.
cb9ed67cb329 Imported from capsule None
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80
5
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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81 @SCREENCASTS@
0
cb9ed67cb329 Imported from capsule None
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82
cb9ed67cb329 Imported from capsule None
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83 **Syntax**
cb9ed67cb329 Imported from capsule None
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84
cb9ed67cb329 Imported from capsule None
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85 - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined.
5
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86 - **Return only records that are joined** returns only the records of the first dataset that join to a record in the second dataset. This is analogous to an INNER JOIN.
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87 - **Return all records of first dataset (fill null with &quot;.&quot;)** returns all intervals of the first dataset, and any intervals that do not join an interval from the second dataset are filled in with a period(.). This is analogous to a LEFT JOIN.
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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88 - **Return all records of second dataset (fill null with &quot;.&quot;)** returns all intervals of the second dataset, and any intervals that do not join an interval from the first dataset are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.**
ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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89 - **Return all records of both datasets (fill nulls with &quot;.&quot;)** returns all records from both datasets, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.**
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90
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91 -----
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92
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93 **Examples**
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94
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95 .. image:: gops_joinRecordsList.gif
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96
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97 Only records that are joined (inner join):
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98
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99 .. image:: gops_joinInner.gif
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100
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101 All records of first dataset:
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102
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103 .. image:: gops_joinLeftOuter.gif
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104
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105 All records of second dataset:
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106
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107 .. image:: gops_joinRightOuter.gif
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108
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109 All records of both datasets:
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110
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111 .. image:: gops_joinFullOuter.gif
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ddf5484243d2 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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112 ]]></help>
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113 </tool>