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Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:18:56 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <macros>
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2 <token name="@VERSION@">0.20.0</token>
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3 <token name="@GALAXY_VERSION@">galaxy0</token>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">csvtk</requirement>
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7 </requirements>
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8 </xml>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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9 <xml name="version_cmd">
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10 <version_command>csvtk version</version_command>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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11 </xml>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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12 <xml name="text_sanitizer">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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13 <sanitizer>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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14 <valid initial="string.printable">
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15 <remove value="&apos;"/>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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16 </valid>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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17 </sanitizer>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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18 </xml>
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19 <xml name="multi_input">
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20 <param type="data" name="in_1" format="csv,tabular"
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21 multiple="true" optional="false"
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22 label="Specify TSV or CSV file inputs"
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23 help="Input tsv or csv files to analyze. HOWEVER, they must all be the **same file type** or the tool will fail/not give correct results!"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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24 />
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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25 </xml>
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26 <xml name="singular_input">
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27 <param type="data" name="in_1" format="csv,tabular"
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28 multiple="false" optional="false"
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29 label="Specify an input TSV or CSV file"
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30 help="Input a TSV or CSV file to work on"
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31 />
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32 </xml>
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33 <xml name="ignore_case">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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34 <param type="boolean" name="ignore_case"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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35 falsevalue="" truevalue="-i"
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36 checked="false"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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37 argument="-i"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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38 label="Ignore cell case?"
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39 help="ABC == abc"
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40 />
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41 </xml>
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42 <xml name="global_parameters">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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43 <section name="global_param" title="csvtk Global Parameters" expanded="false">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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44 <param type="boolean" name="header"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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45 falsevalue="-H" truevalue=""
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46 checked="true"
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47 argument="-H"
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48 label="Input file has a header line"
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49 />
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50 <param type="boolean" name="illegal_rows"
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51 falsevalue="" truevalue="-I"
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52 checked="false"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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53 argument="-I"
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54 label="Ignore illegal rows"
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55 help="Use if file has illegal rows as defined in the help section"
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56 />
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57 <param type="boolean" name="empty_rows"
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58 falsevalue="" truevalue="-E"
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59 checked="false"
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60 argument="-E"
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61 label="Ignore empty rows"
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62 help="Ignore rows with no data (only needed if input has empty rows)"
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63 />
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64 <param type="boolean" name="lazy_quotes"
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65 falsevalue="" truevalue="-l"
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66 checked="false"
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67 argument="-l"
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68 label="File has Lazy quotes"
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69 help="(TSV files only) If Yes, a quote may appear in an unquoted field and a non-doubled quote may appear in a quoted field"
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70 />
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71 </section>
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72 </xml>
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73 <xml name="fields_input">
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74 <conditional name="column_text" >
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75 <param type="select" name="select" label="Select input column(s) based on" argument="-F -f">
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76 <option value="string">Column Name(s)</option>
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77 <option value="column">Column Number(s)</option>
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78 </param>
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79 <when value="column">
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80 <param type="data_column" name="in_text"
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81 data_ref="in_1"
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82 multiple="true"
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83 label="Input column number(s)"
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84 help="Select column(s) to use for analysis"
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85 />
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86 </when>
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87 <when value="string">
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88 <param type="text" name="in_text"
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89 optional="false"
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90 label="Input column name(s)"
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91 help="Multiple columns can be given if separated by a ' , '.
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92 Column numbers can be given too - ex. '1,2' will target columns 1 and 2.
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93 Please see the help section below for more detailed info">
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94 <sanitizer>
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95 <valid initial="string.printable">
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96 <remove value="&apos;"/>
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97 </valid>
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98 </sanitizer>
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99 </param>
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100 </when>
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101 </conditional>
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102 </xml>
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103 <xml name="singular_fields_input">
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diff changeset
104 <conditional name="column_text" >
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105 <param type="select" name="select" label="Select input column based on" argument="-f">
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106 <option value="string">Column Name</option>
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107 <option value="column">Column Number</option>
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108 </param>
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109 <when value="column">
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110 <param type="data_column" name="in_text"
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111 data_ref="in_1"
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112 multiple="false"
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113 label="Input column number"
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114 help="Select column to use for analysis"
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115 />
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116 </when>
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117 <when value="string">
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118 <param type="text" name="in_text"
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119 optional="false"
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120 label="Input column name"
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121 help="Input column name or number ex. 'Length' or '1'.
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122 Please see the help section below for more detailed info">
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123 <sanitizer>
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124 <valid initial="string.printable">
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125 <remove value="&apos;"/>
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126 </valid>
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127 </sanitizer>
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128 </param>
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129 </when>
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130 </conditional>
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131 </xml>
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132 <xml name="plot_field">
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133 <conditional name="column_text" >
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134 <param type="select" name="select" label="Select input data column based on" argument="-f">
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135 <option value="string">Column Name</option>
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136 <option value="column">Column Number</option>
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137 </param>
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138 <when value="column">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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139 <param type="data_column" name="in_text"
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140 data_ref="in_1"
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141 multiple="false"
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142 label="Input data column number"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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143 />
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144 </when>
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diff changeset
145 <when value="string">
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146 <param type="text" name="in_text"
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147 optional="false"
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148 label="Input data column name"
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149 help="Can use column name or column number">
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150 <sanitizer>
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151 <valid initial="string.printable">
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diff changeset
152 <remove value="&apos;"/>
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153 </valid>
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154 </sanitizer>
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155 </param>
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156 </when>
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157 </conditional>
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158 </xml>
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159 <xml name="groups_input">
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160 <conditional name="group_field" >
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161 <param type="select" name="select_group" label="Select column to group data" argument="-g" optional="false" help="Specify a single column that is used to create data groups. An example is shown in the help section">
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162 <option value="none">None</option>
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163 <option value="string">Column Name</option>
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164 <option value="column">Column Number</option>
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165 </param>
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166 <when value="none" />
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167 <when value="column">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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168 <param type="data_column" name="in_text"
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169 data_ref="in_1"
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170 multiple="false"
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171 label="Group by column number"
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172 />
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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173 </when>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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174 <when value="string">
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175 <param type="text" name="in_text"
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176 optional="false"
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177 label="Group by column name"
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178 help="Can use column name or number">
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179 <sanitizer>
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180 <valid initial="string.printable">
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181 <remove value="&apos;"/>
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182 </valid>
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183 </sanitizer>
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184 </param>
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185 </when>
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186 </conditional>
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187 </xml>
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188 <xml name="global_plot_parameters">
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189 <section name="plot_parameters" title="Advanced Optional Plot Parameters" expanded="false">
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190 <param type="float" name="figure_height"
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191 argument="--height"
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192 optional="true"
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193 label="Figure Height (Default 4.5)"
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194 />
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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195 <param type="float" name="figure_width"
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196 argument="--width"
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197 optional="true"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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198 label="Figure Width (Default 1.5)"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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199 />
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200 <param type="float" name="tick_width"
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201 argument="--tick-width"
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202 optional="true"
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203 label="Axis Tick Width (Default 1.5)"
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204 />
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205 <param type="text" name="title"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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206 argument="--title"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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207 optional="true"
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208 label="Specify Figure Title">
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209 <sanitizer>
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210 <valid initial="string.printable">
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211 <remove value="&apos;"/>
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212 </valid>
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213 </sanitizer>
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214 </param>
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215 <param type="text" name="x_label"
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216 argument="--xlab"
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217 optional="true"
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218 label="Specify X-axis label">
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219 <sanitizer>
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220 <valid initial="string.printable">
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221 <remove value="&apos;"/>
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222 </valid>
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223 </sanitizer>
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224 </param>
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225 <param type="float" name="min_x"
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226 argument="--x-min"
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227 optional="true"
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228 label="Minimum value of X-axis (float)"
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229 />
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230 <param type="float" name="max_x"
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231 argument="--x-max"
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232 optional="true"
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233 label="Maximum value of X-axis (float)"
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234 />
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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235 <param type="text" name="y_label"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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236 argument="--ylab"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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237 optional="true"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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238 label="Specify Y-axis label">
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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239 <sanitizer>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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240 <valid initial="string.printable">
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241 <remove value="&apos;"/>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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242 </valid>
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243 </sanitizer>
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244 </param>
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245 <param type="float" name="min_y"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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246 argument="--y-min"
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247 optional="true"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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248 label="Minimum value of Y-axis (float)"
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249 />
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250 <param type="float" name="max_y"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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251 argument="--y-max"
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252 optional="true"
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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253 label="Maximum value of Y-axis (float)"
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254 />
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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255 </section>
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256 </xml>
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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257 <token name="@HELP_COLUMNS@">
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258 Column Name Input Help
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259 ######################
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260
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261 - Multiple names can be given if separated by a ' , '.
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262
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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263 - ex. 'ID,Organism' would target the columns named ID and Organism for the function
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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264
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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265 - Column names are case SeNsitive
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266
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267 - Column numbers can also be given:
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268
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269 -ex. '1,2,3' or '1-3' for inputting columns 1-3.
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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270
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271 - You can also specify all but unwanted column(s) with a ' - '.
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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272
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273 - ex. '-ID' would target all columns but the ID column
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274
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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275 ----
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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276 </token>
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277 <token name="@HELP_INPUT_DATA@">
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278 Input Data
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279 ##########
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280
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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281 ::
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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282
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283 **Limitations of Input Data**
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284
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285 1. The CSV parser requires all the lines have same number of fields/columns.
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286 If your file has illegal rows, set the "Illegal Rows" parameter to "Yes" to pass your data through
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287 Even lines with spaces will cause error.
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288 Example bad table below.
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289
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290 2. By default, csvtk thinks files have header rows. If your file does not, set global parameter
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291 "Has Header Row" to "No"
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292
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293 3. Column names should be unique and are case sensitive!
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294
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295 4. Lines starting with "#" or "$" will be ignored, if in the header row
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296
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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297 5. If " exists in tab-delimited files, set Lazy quotes global parameter to "Yes"
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298
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299 Example bad table:
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300
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301 +--------+--------+--------+--------+
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302 | Head 1 | Head 2 | Head 3 | Head 3 |
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303 +========+========+========+========+
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304 | 1 | 2 | 3 | |
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305 +--------+--------+--------+--------+
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306 | this | will | | break |
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307 +--------+--------+--------+--------+
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308
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309 Bad tables may work if both the "Ignore Illegal Rows" and "Ignore Empty Rows" global parameters are set to "Yes",
7ff05a1ffdd7 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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310 But there is no guarentee of that!
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311
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312 ----
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313 </token>
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314 <token name="@HELP_END_STATEMENT@">
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315 More Information
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316 ################
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317 For information from the creators of csvtk, please visit their site at: https://bioinf.shenwei.me/csvtk/
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318
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319 Although be aware that some features may not be available and some small changes were made to work with Galaxy.
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320
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321 **Notable changes from their documentation:**
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322
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323 - Cannot specify multiple file header names (IE cannot use "name;username" as a valid column match)
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324
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325 - No single quotes / apostrophes allowed in text inputs
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326 </token>
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327 <xml name="citations">
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328 <citations>
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329 <citation type="bibtex">@ARTICLE{a1,
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330 title = {csvtk - CSV/TSV Toolkit},
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331 author = {Wei Shen},
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332 url = {https://github.com/shenwei356/csvtk}
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333 }
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334 }</citation>
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335 </citations>
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336 </xml>
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337 </macros>