Mercurial > repos > nml > csvtk_cut

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:09:36 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 <tool id="csvtk_cut" name="csvtk-cut" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> and keep selected columns</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
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14 csvtk cut --num-cpus "\${GALAXY_SLOTS:-1}"
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15
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16 ## Add additional flags as specified ##
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17 #######################################
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18 $ignore_case
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19 $global_param.illegal_rows
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20 $global_param.empty_rows
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21 $global_param.header
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22 $global_param.lazy_quotes
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24 ## Set Tabular input/output flag if input is tabular ##
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25 #######################################################
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26 #if $in_1.is_of_type("tabular"):
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27 -t -T
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28 #end if
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29
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30 ## Set Input ##
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31 ###############
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32 '$in_1'
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33
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34 ## Specify fields for collapse ##
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35 #################################
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36 -F -f '$column_text.in_text'
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37
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38 ## To output ##
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39 ###############
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40 > cut
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41
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42 ]]></command>
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43 <inputs>
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44 <expand macro="singular_input" />
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45 <expand macro="fields_input" />
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46 <expand macro="ignore_case" />
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47 <expand macro="global_parameters" />
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48 </inputs>
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49 <outputs>
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50 <data format_source="in_1" name="cut" from_work_dir="cut" label="${in_1.name} cut out column(s) ${column_text.in_text}" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="in_1" value="plot.csv" />
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55 <conditional name="column_text">
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56 <param name="select" value="column" />
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57 <param name="in_text" value="2,3" />
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58 </conditional>
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59 <output name="cut" file="cut_1.csv" ftype="csv" />
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60 </test>
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61 <test>
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62 <param name="in_1" value="plot.csv" />
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63 <conditional name="column_text">
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64 <param name="select" value="string" />
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65 <param name="in_text" value="-2" />
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66 </conditional>
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67 <output name="cut" file="cut_2.csv" ftype="csv" />
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71
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72 Csvtk - Cut Help
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73 ----------------
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74
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75 Info
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76 ####
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77
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78 Csvtk Cut cuts specified columns to create an output
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79
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80 Csvtk Cut can be used to keep columns with normal inputs such as the column name or number. It
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81 can also be used to specify columns to remove with a "-" at the start. An example can be seen below.
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82
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83 .. class:: warningmark
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84
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85 Single quotes are not allowed in text inputs!
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86
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87 @HELP_INPUT_DATA@
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88
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89
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90 Usage
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91 #####
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92
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93 To run csvtk-cut, all you need is a valid (as defined above) CSV or TSV file
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94
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95 **Example cut to keep columns**
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96
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97 Input table:
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98
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99 +--------+--------+----------+
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100 | Name | Colour | Food |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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101 +========+========+==========+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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102 | Eric | Blue | Apples |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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103 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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104 | Darian | Blue | Pancakes |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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105 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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106 | Daniel | Red | Apples |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
107 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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108 | Emily | Blue | Apples |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
109 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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110
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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111 Now if we wanted to cut out and keep columns 1 and 2, our column input string (-F -f) would be "1,2"
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
112 and would result in the following table:
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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113
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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114 +--------+--------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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115 | Name | Colour |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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116 +========+========+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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117 | Eric | Blue |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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118 +--------+--------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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119 | Darian | Blue |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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120 +--------+--------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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121 | Daniel | Red |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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122 +--------+--------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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diff changeset
123 | Emily | Blue |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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124 +--------+--------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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125
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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126 --------
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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127
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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128 **Example cut to remove column**
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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129
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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130 Similar input table as above:
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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131
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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132 +--------+--------+----------+-----------------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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133 | Name | Colour | Food | Unneeded Column |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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134 +========+========+==========+=================+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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135 | Eric | Blue | Apples | fadah |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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136 +--------+--------+----------+-----------------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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137 | Darian | Blue | Pancakes | ewq3rfa |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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138 +--------+--------+----------+-----------------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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139 | Daniel | Red | Apples | feda356t |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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140 +--------+--------+----------+-----------------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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141 | Emily | Blue | Apples | a342qadef |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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142 +--------+--------+----------+-----------------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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143
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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144 Now, we have a garbage last column and we want to keep everything else. We could input "1,2,3" to keep the first 3 columns,
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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145 OR if we set the input column name to "-4" or "-Unneeded Column" csvtk cut will remove the final column giving the following:
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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146
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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147 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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148 | Name | Colour | Food |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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149 +========+========+==========+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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150 | Eric | Blue | Apples |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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151 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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152 | Darian | Blue | Pancakes |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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153 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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154 | Daniel | Red | Apples |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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155 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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156 | Emily | Blue | Apples |
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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157 +--------+--------+----------+
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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158
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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159 ----
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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160
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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161 @HELP_COLUMNS@
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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162
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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163
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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164 @HELP_END_STATEMENT@
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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165
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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166
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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167 ]]></help>
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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168 <expand macro="citations" />
5b5330a8dfac "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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169 </tool>