Mercurial > repos > nml > csvtk_separate

annotate separate.xml @ 0:1be50033b476 draft default tip

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 17:24:41 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_separate" name="csvtk-separate" version="@VERSION@+@GALAXY_VERSION@">
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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2 <description> column into multiple columns</description>
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3 <macros>
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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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" />
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 #set column_number = $column_names.count(',') + 1
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11
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12 ###################
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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13 ## Start Command ##
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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14 ###################
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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15 csvtk separate --num-cpus "\${GALAXY_SLOTS:-1}"
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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16
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17 ## Add additional flags as specified ##
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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18 #######################################
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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19 $ignore_case
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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20 $global_param.illegal_rows
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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21 $global_param.empty_rows
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22 $global_param.header
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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23 $global_param.lazy_quotes
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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24
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25 ## Set Tabular input/output flag if first input is tabular ##
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26 #############################################################
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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27 #if $in_1.is_of_type("tabular"):
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28 -t -T
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29 #end if
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30
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31 ## Set input files ##
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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32 #####################
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33 $in_1
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34
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35 ## Specify field to use ##
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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36 ##########################
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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37 -f '$column_text.in_text'
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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38
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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39 ## Specific inputs ##
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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40 #####################
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41 -n '$column_names'
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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42 -N '$column_number'
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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43
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44 #if $how_separate.how == 'sep'
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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45 -s '$how_separate.separator'
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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46 #else
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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47 -r '($how_separate.separator)'
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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48 #end if
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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49
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50 --na '$fill_na'
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51 $extra_data
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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52 $remove
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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53
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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54 ## To output ##
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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55 ###############
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56 > separated
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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57
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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58 ]]></command>
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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59 <inputs>
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60 <expand macro="singular_input"/>
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61 <expand macro="singular_fields_input"/>
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62 <conditional name="how_separate">
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63 <param name="how" type="select" label="Separate input column by:">
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64 <option value="sep">Separator String</option>
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65 <option value="regex">Regexp</option>
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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66 </param>
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67 <when value="sep">
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68 <param name="separator" type="text" value="; " argument="-s"
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69 label="Separator string"
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70 help="Specify what string separates the data in the column">
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71 <expand macro="text_sanitizer" />
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72 </param>
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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73 </when>
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74 <when value="regex">
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75 <param name="separator" type="text" value=".+" argument="-r"
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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76 label="Set regex search pattern"
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77 help="Use regex to match input column information. Example: ^(.+)$ will match all characters.
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78 Regex help can be found below. The ' character is invalid">
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79 <expand macro="text_sanitizer" />
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80 </param>
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81 </when>
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82 </conditional>
1be50033b476 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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83 <param name="column_names" type="text" value="new1,new2" argument="-n"
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84 label="Specify new column name(s)"
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85 help="More than one column can be made by separating the names by a comma (,). Ex. 'Genus,Species' would create two columns.">
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86 <expand macro="text_sanitizer" />
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87 </param>
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88 <param name="extra_data" type="select" label="Handle extra data by:"
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89 help="Extra data is data that does not fit into the new columns made. An example can be found below">
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90 <option value="--drop">Dropping it</option>
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91 <option value="--merge">Merging it</option>
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92 </param>
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93 <param name="fill_na" type="text" value="NA" argument="--na"
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94 label="Character string to fill empty columns">
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95 <expand macro="text_sanitizer" />
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96 </param>
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97 <param name="remove" type="boolean" checked="true" argument="-R"
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98 truevalue="-R"
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99 falsevalue=""
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100 label="Remove input column"
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101 />
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102 <expand macro="ignore_case" />
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103 <expand macro="global_parameters" />
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104 </inputs>
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105 <outputs>
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106 <data format_source="in_1" from_work_dir="separated" name="separated" label="${in_1.name} column ${column_text.in_text} separated by ${how_separate.separator}" />
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107 </outputs>
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108 <tests>
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109 <test>
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110 <param name="in_1" value="collapsed.tsv" />
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111 <conditional name="column_text">
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112 <param name="select" value="string" />
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113 <param name="in_text" value="2" />
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114 </conditional>
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115 <conditional name="how_separate">
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116 <param name="how" value="sep" />
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117 <param name="separator" value="; " />
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118 </conditional>
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119 <param name="column_names" value="1,2" />
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120 <param name="fill_na" value="NA" />
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121 <param name="extra_data" value="--drop" />
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122 <param name="remove" value="true" />
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123 <output name="separated" file="separated_1.tsv" ftype="tabular" />
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124 </test>
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125 <test>
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126 <param name="in_1" value="collapsed.tsv" />
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127 <conditional name="column_text">
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128 <param name="select" value="string" />
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129 <param name="in_text" value="2" />
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130 </conditional>
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131 <conditional name="how_separate">
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132 <param name="how" value="sep" />
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133 <param name="separator" value="; " />
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134 </conditional>
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135 <param name="column_names" value="1,2" />
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136 <param name="fill_na" value="N/A" />
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137 <param name="extra_data" value="--merge" />
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138 <param name="remove" value="false" />
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139 <output name="separated" file="separated_2.tsv" ftype="tabular" />
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140 </test>
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141 </tests>
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142 <help><![CDATA[
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143
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144 Csvtk - Separate Help
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145 ---------------------
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146
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147 Info
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148 ####
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149
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150 Csvtk-separate separates columns into new columns based on either an input string or a regex expression.
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151
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152 The regex input for this tool is structured such that your regular expression **does not** need to start with with quotes or brackets. You can
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153 start your expression with a `^` or just go straight into it
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154
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155 For example:
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156
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157 ::
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158
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159 Using `.+` as an input would be used in the code as '(.+)'
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160
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161 Using ^(.+)$ as an input would yield an input in the code as '(^(.+)$)'
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162
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163 .. class:: warningmark
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164
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165 Single quotes are not allowed in text inputs!
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166
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167 ----
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168
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169
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170 @HELP_INPUT_DATA@
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171
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172
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173 Usage
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174 #####
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175
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176 **Ex. Separate with Dropping Data**
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177
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178 Suppose we had the following table and wanted to separate the scientific name column to create two new columns called genus and species:
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179
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180 +------------+------------------------------+
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181 | Name | Scientific Name |
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182 +============+==============================+
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183 | Red Fox | Vulpes vulpes |
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184 +------------+------------------------------+
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185 | Salmonella | Salmonella enterica enterica |
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186 +------------+------------------------------+
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187
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188 First, we set our separator to string and use just a space (' ') as the separator as the names are separated by spaces.
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189
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190 Then, we have to set the new column names which can be done by setting the column names to 'Genus,Species' (make sure that the names are
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191 separated by a comma).
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192
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193 Finally, we have to decide if we want to drop the input column and if we want to merge the additional data or drop it.
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194
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195 First table will show dropping of additional data (the second enterica is additional as it cannot fit in its own column)
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196
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197 +------------+------------+----------+
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198 | Name | Genus | Species |
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199 +============+============+==========+
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200 | Red Fox | Vulpes | vulpes |
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201 +------------+------------+----------+
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202 | Salmonella | Salmonella | enterica |
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203 +------------+------------+----------+
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204
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205 |
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206
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207 Here is what it would look like if we merged data instead:
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208
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209 +------------+------------+-------------------+
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210 | Name | Genus | Species |
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211 +============+============+===================+
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212 | Red Fox | Vulpes | vulpes |
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213 +------------+------------+-------------------+
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214 | Salmonella | Salmonella | enterica enterica |
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215 +------------+------------+-------------------+
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217 ----
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219
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220 @HELP_COLUMNS@
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221
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223 @HELP_END_STATEMENT@
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225
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226 ]]></help>
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227 <expand macro="citations" />
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228 </tool>