Mercurial > repos > nml > csvtk_gather

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:21:15 -0400
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0
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1 <tool id="csvtk_gather" name="csvtk-gather" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> column(s) into key-value pairs</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 ###################
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11 ## Start Command ##
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12 ###################
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13 csvtk gather --num-cpus "\${GALAXY_SLOTS:-1}"
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14
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15 ## Add additional flags as specified ##
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16 #######################################
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17 $global_param.illegal_rows
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18 $global_param.empty_rows
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19 $global_param.header
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20 $global_param.lazy_quotes
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21
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22 ## Set Tabular input/output flag if first input is tabular ##
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23 #############################################################
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24 #if $in_1.is_of_type("tabular"):
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25 -t -T
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26 #end if
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27
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28 ## Set input files ##
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29 #####################
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30 $in_1
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31
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32 ## Specify fields to use ##
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33 ###########################
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34 -F -f '$column_text.in_text'
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35
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36 ## Specific inputs ##
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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37 #####################
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38 -k '$key_string'
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39 -v '$value_string'
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40
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41 ## Keep only Key/value columns ##
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42 #################################
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43 #if $only_input_columns == 'Yes'
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44 | csvtk cut -F -f '$key_string','$value_string'
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45
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46 #if $in_1.is_of_type("tabular"):
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47 -t -T
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48 #end if
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49 #end if
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50
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51 ## To output ##
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52 ###############
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53 > gathered
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54
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55 ]]></command>
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56 <inputs>
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57 <expand macro="singular_input"/>
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58 <expand macro="fields_input"/>
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59 <param name="key_string" type="text"
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60 optional="false"
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61 argument="-k"
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62 label="Name of Key Column"
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63 help="Set name of key column that gathered field will output to">
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64 <expand macro="text_sanitizer" />
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65 </param>
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66 <param name="value_string" type="text"
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67 optional="false"
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68 argument="-v"
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69 label="Name of Value Column">
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70 <expand macro="text_sanitizer" />
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71 </param>
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72 <param name="only_input_columns" type="boolean"
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73 truevalue="Yes"
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74 falsevalue="No"
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75 label="Keep only Key and Value column(s) generated"
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76 help="Removes all columns but the input labeled key and value columns"
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77 />
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78 <expand macro="global_parameters" />
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79 </inputs>
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80 <outputs>
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81 <data format_source="in_1" from_work_dir="gathered" name="gathered" label="${in_1.name} gathered on column(s) ${column_text.in_text}" />
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="in_1" value="csv.csv" />
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86 <param name="key_string" value="1" />
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87 <param name="value_string" value="2" />
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88 <conditional name="column_text">
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89 <param name="select" value="string" />
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90 <param name="in_text" value="1" />
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91 </conditional>
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92 <output name="gathered" file="gathered.csv" ftype="csv" />
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96
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97 Csvtk - Gather Help
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98 -------------------
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99
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100 Info
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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101 ####
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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102
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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103 Csvtk gather gathers columns into key-value pairs
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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104
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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105 .. class:: warningmark
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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106
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
107 Single quotes are not allowed in text inputs!
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
108
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
109 @HELP_INPUT_DATA@
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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110
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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111
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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112 Usage
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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113 #####
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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114
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
115 **Ex. Gather with column 1:**
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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116
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
117 Suppose we had the following table:
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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118
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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119 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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120 | Name | Blood Type | Frequency |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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121 +=========+============+===========+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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122 | Bob | A | 4 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
123 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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124 | Jacob | B | 5 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
125 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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126 | Matthew | O | 12 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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127 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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128 | Daniel | AB | 1 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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129 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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130
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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131 If we did a gather on column 1 creating a key column called "Key" and a value column called "Output"
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
132 we would get the following result.
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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133
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
134 +------------+-----------+------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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135 | Blood Type | Frequency | Key | Output |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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136 +============+===========+======+=========+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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137 | A | 4 | Name | Bob |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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138 +------------+-----------+------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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139 | B | 4 | Name | Jacob |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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140 +------------+-----------+------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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141 | O | 12 | Name | Matthew |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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142 +------------+-----------+------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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143 | AB | 1 | Name | Daniel |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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144 +------------+-----------+------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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145
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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146 ----
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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147
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
148 **Ex. Gather with 2 columns:**
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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149
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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150 Same starting table
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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151
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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152 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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153 | Name | Blood Type | Frequency |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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154 +=========+============+===========+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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155 | Bob | A | 4 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
156 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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157 | Jacob | B | 5 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
158 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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159 | Matthew | O | 12 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
160 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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161 | Daniel | AB | 1 |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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162 +---------+------------+-----------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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163
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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164 Now, if we specify the input columns as "1,2" to get columns 1 and 2 targeted as the key columns (called key),
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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165 we get the following output:
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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166
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
167 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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168 | Frequency | Key | Output |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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169 +===========+============+=========+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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170 | 4 | Name | Bob |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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171 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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172 | 4 | Blood Type | A |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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173 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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174 | 4 | Name | Jacob |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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175 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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176 | 4 | Blood Type | B |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
177 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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178 | 12 | Name | Matthew |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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179 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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180 | 12 | Blood Type | O |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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181 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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182 | 1 | Name | Daniel |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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183 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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184 | 1 | Blood Type | AB |
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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185 +-----------+------------+---------+
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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186
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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187 ----
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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188
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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189 @HELP_COLUMNS@
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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190
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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191
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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192 @HELP_END_STATEMENT@
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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193
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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194
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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195 ]]></help>
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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196 <expand macro="citations" />
6acd7c0ad672 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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197 </tool>