Mercurial > repos > nml > csvtk_split

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:18:02 -0400
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1 <tool id="csvtk_split" name="csvtk-split" version="@VERSION@+@GALAXY_VERSION@">
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2 <description>table into multiple files</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 <expand macro="version_cmd" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 ## Create directory and set input name ##
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11 #########################################
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12 mkdir -p ./output &&
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14 #set input_name = str($in_1.name)
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15 ln -s '$in_1' $input_name &&
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17 ###################
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18 ## Start Command ##
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19 ###################
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21 csvtk split -o ./output --num-cpus "\${GALAXY_SLOTS:-1}"
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23 ## Add additional flags as specified ##
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24 #######################################
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25 $ignore_case
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26 $global_param.illegal_rows
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27 $global_param.empty_rows
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28 $global_param.header
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29 $global_param.lazy_quotes
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30
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31 ## Set Tabular input/output flag if input is tabular ##
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32 #######################################################
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33 #if $in_1.is_of_type("tabular"):
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34 -t -T
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35 #end if
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36
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37 ## Set Input ##
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38 ###############
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39 '$input_name'
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40
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41 ## Specify fields for splitting ##
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42 ##################################
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43 -F -f '$column_text.in_text'
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44
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45 ]]></command>
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46 <inputs>
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47 <expand macro="singular_input" />
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48 <expand macro="fields_input" />
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49 <expand macro="ignore_case" />
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50 <expand macro="global_parameters" />
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51 </inputs>
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52 <outputs>
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53 <collection name="list_split" type="list" label="${in_1.name} split on column ${column_text.in_text}">
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54 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="false" format="csv,tabular"/>
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55 </collection>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="in_1" value="csv.csv" />
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60 <conditional name="column_text">
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61 <param name="select" value="string" />
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62 <param name="in_text" value="1" />
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63 </conditional>
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64 <param name="ignore_case" value="true" />
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65 <output_collection name="list_split" type="list">
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66 <element name="csv-bob" file="csv-bob.csv" ftype="csv" />
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67 <element name="csv-darian" file="csv-darian.csv" ftype="csv" />
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68 <element name="csv-jack" file="csv-jack.csv" ftype="csv" />
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69 </output_collection>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73
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74 Csvtk - Split Help
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75 ------------------
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76
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77 Info
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78 ####
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79 Split input csv/tsv files into multiple csv/tsv files based on a column number(s) or name(s).
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80
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81 This tool will generate as many output files as there are unique data points in the selected column(s).
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82
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83 Examples below.
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84
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85 .. class:: warningmark
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86
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87 Single quotes are not allowed in text inputs!
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88
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89 @HELP_INPUT_DATA@
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90
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91
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92 Usage
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93 #####
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94 Here we will demonstrate what the tool does when 1 column is selected or when 2+ columns are selected.
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95
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96 **Ex. Split input based on column 1:**
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97
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98 ::
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99
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100 Suppose we have the following input table that we want to split on column 2, the 'Colour' column:
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101
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102 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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103 | Name | Colour | Food |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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104 +========+========+==========+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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105 | Eric | Blue | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
106 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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107 | Darian | Blue | Pancakes |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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108 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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109 | Daniel | Red | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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110 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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111 | Frank | Blue | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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112 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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113
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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114 --------------------------------------------------------------------------------
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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115
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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116 Splitting would yield the following 2 tables:
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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117
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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118 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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119 | Name | Colour | Food |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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120 +========+========+==========+ +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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121 | Eric | Blue | Apples | | Name | Colour | Food |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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122 +--------+--------+----------+ + +========+========+==========+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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123 | Darian | Blue | Pancakes | | Daniel | Red | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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124 +--------+--------+----------+ +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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125 | Frank | Blue | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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126 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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127
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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128 ---------------------------------------------------------------------------------
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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129
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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130 ----
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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131
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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132 **Ex. Split on 2 columns:**
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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133
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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134 ::
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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135
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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136 Suppose keep the same input but instead split on both the 'Colour' and 'Food' columns:
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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137
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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138 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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139 | Name | Colour | Food |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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140 +========+========+==========+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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141 | Eric | Blue | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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142 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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143 | Darian | Blue | Pancakes |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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144 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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145 | Daniel | Red | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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146 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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147 | Frank | Blue | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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148 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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149
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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150 --------------------------------------------------------------------------------------------------------
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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151
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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152 This split would yield the following three output files:
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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153
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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154 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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155 | Name | Colour | Food | +--------+--------+----------+ +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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156 +========+========+==========+ | Name | Colour | Food | | Name | Colour | Food |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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157 | Eric | Blue | Apples | + +========+========+==========+ + +========+========+==========+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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158 +--------+--------+----------+ | Darian | Blue | Pancakes | | Daniel | Red | Apples |
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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159 | Frank | Blue | Apples | +--------+--------+----------+ +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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160 +--------+--------+----------+
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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161
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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162 Here, the value in the cell has to match for both columns for them to be output together. Frank and Eric
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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163 like apples and the colour blue so they get put together. And even though Darian likes the colour blue, he
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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164 prefers pancakes and thus gets his own output file.
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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165
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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166 ----
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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167
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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168 @HELP_END_STATEMENT@
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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169
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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170
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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171 ]]></help>
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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172 <expand macro="citations" />
92509cf500a4 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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173 </tool>