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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit d7b1a60c0aecc46b7f625c3e32f882562b512fd9
author devteam
date Mon, 13 Jun 2022 16:24:31 +0000
parents 0145969324c4
children
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1
7bf44b9d7a8b Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_subtract_1" name="Subtract" version="1.0.0">
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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2 <description>the intervals of two datasets</description>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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3 <macros>
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devteam
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4 <import>macros.xml</import>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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5 </macros>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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6 <expand macro="requirements" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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7 <code file="operation_filter.py"/>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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8 <command><![CDATA[
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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9 python '$__tool_directory__/gops_subtract.py'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 '$input1'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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11 '$input2'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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12 '$output'
0
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13
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 #if $input1.is_of_type('gff')
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 -1 1,4,5,7 --gff1
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract 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}
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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18 #end if
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19
5
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20 #if $input2.is_of_type('gff')
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 -2 1,4,5,7 --gff2
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 #else:
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 #end if
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25
5
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26 -m $min
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 $returntype
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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28 ]]></command>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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29 <inputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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30 <param name="input2" type="data" format="interval,gff" label="Subtract" help="Second dataset" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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31 <param name="input1" type="data" format="interval,gff" label="from" help="First dataset" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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32 <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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33 <option value="">Intervals with no overlap</option>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 <option value="-p">Non-overlapping pieces of intervals</option>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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35 </param>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 <param name="min" type="integer" value="1" min="1" label="where minimal overlap is" help="(bp)" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 </inputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 <outputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 <data name="output" format_source="input1" metadata_source="input1"/>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 </outputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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41 <tests>
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42 <test>
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43 <param name="input1" value="1.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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44 <param name="input2" value="2.bed" />
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45 <param name="min" value="1" />
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46 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 <output name="output" file="gops-subtract.dat" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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48 </test>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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49 <test>
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50 <param name="input1" value="1.bed" />
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51 <param name="input2" value="2_mod.bed" ftype="interval"/>
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52 <param name="min" value="1" />
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53 <param name="returntype" value="" />
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54 <output name="output" file="gops_subtract_diffCols.dat" />
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55 </test>
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56 <test>
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57 <param name="input1" value="gops_subtract_bigint.bed" />
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58 <param name="input2" value="2.bed" />
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59 <param name="min" value="1" />
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60 <param name="returntype" value="" />
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61 <output name="output" file="gops-subtract.dat" />
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62 </test>
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63 <test>
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64 <param name="input1" value="1.bed" />
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65 <param name="input2" value="2.bed" />
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66 <param name="min" value="10" />
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67 <param name="returntype" value="Non-overlapping pieces of intervals" />
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68 <output name="output" file="gops-subtract-p.dat" />
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69 </test>
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70 <!-- Subtract two GFF files. -->
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71 <test>
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72 <param name="input1" value="gops_subtract_in1.gff" />
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73 <param name="input2" value="gops_subtract_in2.gff" />
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74 <param name="min" value="1" />
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75 <param name="returntype" value="" />
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76 <output name="output" file="gops_subtract_out1.gff" />
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77 </test>
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78 <!-- Subtract BED file from GFF file. -->
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79 <test>
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80 <param name="input1" value="gops_subtract_in1.gff" />
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81 <param name="input2" value="gops_subtract_in2.bed" />
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82 <param name="min" value="1" />
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83 <param name="returntype" value="" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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84 <output name="output" file="gops_subtract_out1.gff" />
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88 .. class:: infomark
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89
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90 **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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91
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92 @SCREENCASTS@
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93
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94 **Syntax**
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95
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96 - **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two datasets.
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97 - **Intervals with no overlap** returns entire intervals from the first dataset that do not overlap the second dataset. The returned intervals are completely unchanged, and this option only filters out intervals that overlap with the second dataset.
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98 - **Non-overlapping pieces of intervals** returns intervals from the first dataset that have the intervals from the second dataset removed. Any overlapping base pairs are removed from the range of the interval. All fields besides start and end are guaranteed to remain unchanged.
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99
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100 -----
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101
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102 **Example**
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103
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104 Intervals with no overlap:
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105
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106 .. image:: gops_subtractOverlappingIntervals.gif
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107
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108 Non-overlapping pieces of intervals:
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109
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110 .. image:: gops_subtractOverlappingPieces.gif
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111 ]]></help>
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112 </tool>