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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:20:19 -0400
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0
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1 <tool id="csvtk_sort" name="csvtk-sort" version="@VERSION@+@GALAXY_VERSION@">
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2 <description> column(s) </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 sort --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 $ignore_case
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18 $global_param.illegal_rows
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19 $global_param.empty_rows
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20 $global_param.header
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21 $global_param.lazy_quotes
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22
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23 ## Set Tabular input/output flag if first input is tabular ##
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24 #############################################################
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25 #if $in_1.is_of_type("tabular"):
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26 -t -T
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27 #end if
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28
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29 ## Set input files ##
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30 #####################
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31 $in_1
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32
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33 ## Set up Sort Repeats ##
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34 ##########################
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35 #for $repeat in $field
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36 -k '$repeat.column_text.in_text':${repeat.sort.sort_type}${repeat.reverse_order}
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37
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38 #if $repeat.sort.sort_type == 'u'
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39 -L '$repeat.column_text.in_text':'$repeat.sort.levels_file'
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40 #end if
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41 #end for
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42
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43 ## To output ##
4a1ea249955e "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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44 ###############
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45 > sorted
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46
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47 ]]></command>
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48 <inputs>
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49 <expand macro="singular_input"/>
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50 <repeat name="field" title="Select Column and Sorting method" min="1" >
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51 <expand macro="singular_fields_input" />
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52 <conditional name="sort">
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53 <param name="sort_type" type="select" label="Sort Type" help="Select how to sort data">
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54 <option value="N">Natural</option>
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55 <option value="n">Numerical</option>
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56 <option value="u">User-Defined (Specify File)</option>
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57 </param>
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58 <when value="N" />
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59 <when value="n" />
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60 <when value="u" >
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61 <param name="levels_file" type="data" format="txt" argument="-L"
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62 optional="false"
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63 label="User defined levels file"
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64 help="If using user defined sorting, specift input text file with one level per line. Example can be found in the help section below."
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65 />
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66 </when>
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67 </conditional>
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68 <param name="reverse_order" type="boolean" argument="r" checked="false"
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69 truevalue="r"
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70 falsevalue=""
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71 label="Reverse Sort"
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72 />
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73 </repeat>
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74 <expand macro="ignore_case" />
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75 <expand macro="global_parameters" />
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76 </inputs>
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77 <outputs>
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78 <data format_source="in_1" from_work_dir="sorted" name="sorted" label="${in_1.name} sorted" />
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="in_1" value="Animals_More.csv" />
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83 <repeat name="field">
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84 <conditional name="column_text">
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85 <param name="select" value="string" />
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86 <param name="in_text" value="2" />
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87 </conditional>
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88 <conditional name="sort">
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89 <param name="sort_type" value="u" />
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90 <param name="levels_file" value="sort_order.txt" />
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91 </conditional>
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92 </repeat>
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93 <repeat name="field">
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94 <conditional name="column_text">
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95 <param name="select" value="string" />
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96 <param name="in_text" value="3" />
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97 </conditional>
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98 <conditional name="sort">
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99 <param name="sort_type" value="n" />
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100 </conditional>
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101 <param name="reverse_order" value="true" />
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102 </repeat>
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103 <repeat name="field">
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104 <conditional name="column_text">
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105 <param name="select" value="string" />
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106 <param name="in_text" value="1" />
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107 </conditional>
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108 <conditional name="sort">
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109 <param name="sort_type" value="N" />
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110 </conditional>
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111 </repeat>
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112 <output name="sorted" value="sorted_1.csv" />
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113 </test>
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114 </tests>
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115 <help><![CDATA[
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116
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117 Csvtk - Sort Help
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118 -----------------
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119
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120 Info
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121 ####
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122
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123 Csvtk-sort sorts columns
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124
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125
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126 .. class:: warningmark
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127
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128 Single quotes are not allowed in text inputs!
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129
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130 ----
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131
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132
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133 @HELP_INPUT_DATA@
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134
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135
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136 Usage
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137 #####
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138
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139 **Ex. Separate with Dropping Data**
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140
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141
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142
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143 ----
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144
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145
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146 @HELP_COLUMNS@
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147
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148
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149 @HELP_END_STATEMENT@
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150
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151
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152 ]]></help>
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153 <expand macro="citations" />
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154 </tool>