Mercurial > repos > nml > csvtk_mutate

annotate mutate.xml @ 0:452fd1614f09 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 17:11:54 -0400
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0
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_mutate" name="csvtk-mutate" version="@VERSION@+@GALAXY_VERSION@">
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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2 <description>new column by regular expression</description>
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3 <macros>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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4 <import>macros.xml</import>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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5 </macros>
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6 <expand macro="requirements" />
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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7 <expand macro="version_cmd" />
452fd1614f09 "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
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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10 ###################
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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11 ## Start Command ##
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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12 ###################
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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13 csvtk mutate --num-cpus "\${GALAXY_SLOTS:-1}"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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14
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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15 ## Add additional flags as specified ##
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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16 #######################################
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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17 $ignore_case
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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18 $global_param.illegal_rows
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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19 $global_param.empty_rows
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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20 $global_param.header
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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21 $global_param.lazy_quotes
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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22
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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23 ## Set Tabular input/output flag if first input is tabular ##
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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24 #############################################################
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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25 #if $in_1.is_of_type("tabular"):
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26 -t -T
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27 #end if
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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28
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29 ## Set input files ##
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30 #####################
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31 '$in_1'
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32
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33 ## Specify fields to use ##
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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34 ###########################
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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35 -f '${column_text.in_text}'
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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36
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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37 ## Column Name and pattern ##
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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38 ############################
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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39 -n '$column_name_input'
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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40 -p '($pattern_input)'
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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41 $remove
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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42 $fill_na
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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43
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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44 ## To output ##
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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45 ###############
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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46 > mutated
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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47
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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48 ]]></command>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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49 <inputs>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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50 <expand macro="singular_input"/>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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51 <conditional name="column_text" >
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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52 <param type="select" name="select" label="Select column based on" argument="-f">
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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53 <option value="string">Column Name</option>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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54 <option value="column">Column Number</option>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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55 </param>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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56 <when value="column">
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57 <param type="data_column" name="in_text"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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58 data_ref="in_1"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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59 multiple="False" force_select="True"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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60 label="Analyze column number"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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61 help="Select column to mutate data from"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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62 />
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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63 </when>
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64 <when value="string">
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65 <param type="text" name="in_text"
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66 optional="False"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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67 label="Analyze column name"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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68 help="Specify column name to pull data out of with Regex"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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69 />
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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70 </when>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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71 </conditional>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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72 <param type="text" name="pattern_input"
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73 value=".+"
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74 argument="-p"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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75 label="Set regex search pattern"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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76 optional="false"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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77 help="Use regex to match input column information. Example: ^(.+)$ will match all characters.
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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78 Regex help can be found below. The ' character is invalid"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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79 >
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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80 <expand macro="text_sanitizer" />
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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81 </param>
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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82 <param type="text" name="column_name_input"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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83 value="new_column"
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84 argument="-n"
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85 label="Set new column name"
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86 optional="false"
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87 help="Specify output column name for the matched data">
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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88 <expand macro="text_sanitizer" />
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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89 </param>
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90 <param type="boolean" name="fill_na"
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91 falsevalue="--na" truevalue=""
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92 checked="true"
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93 label="Fill Non-matches"
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94 help="If NO, mutate will create a blank cell where no regex matches (--na). If YES the full cell value will be copied of non-matched columns"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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95 />
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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96 <param name="remove" type="boolean" checked="false"
452fd1614f09 "planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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97 falsevalue=""
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98 truevalue="-R"
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99 argument="-R"
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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" name="mutated" from_work_dir="mutated"
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107 label='${in_1.name} mutated by column ${column_text.in_text} with pattern ${pattern_input}' />
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108 </outputs>
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109 <tests>
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110 <test>
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111 <param name="in_1" value="blood_type.tsv" />
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112 <conditional name="column_text">
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113 <param name="select" value="string" />
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114 <param name="in_text" value="1" />
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115 </conditional>
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116 <param name="column_name_input" value="new_column" />
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117 <param name="pattern_input" value=".*" />
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118 <output name="mutated" file="mutated.tsv" ftype="tabular" />
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119 </test>
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120 <test>
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121 <param name="in_1" value="blood_type.tsv" />
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122 <conditional name="column_text">
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123 <param name="select" value="string" />
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124 <param name="in_text" value="1" />
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125 </conditional>
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126 <param name="column_name_input" value="new_column" />
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127 <param name="pattern_input" value="Darian" />
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128 <param name="remove" value="true" />
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129 <param name="fill_na" value="false" />
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130 <output name="mutated" file="mutate_removed.tsv" ftype="tabular" />
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134
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135 Csvtk - Mutate Help
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136 -------------------
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137
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138 Info
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139 ####
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140 Csvtk-mutate is a tool that uses Regular Expressions (Regex) to match data in the specified column. Using this matched data, a
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141 new column is created using that matched data.
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142
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143 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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144 start your expression with a `^` or just go straight into it
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145
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146 For example:
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147
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148 ::
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149
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150 Using `.+` as an input would be used in the code as '(.+)'
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151
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152 Using ^(.+)$ as an input would yield an input in the code as '(^(.+)$)'
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153
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154 .. class:: warningmark
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155
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156 Single quotes are not allowed in text inputs!
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157
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158 -----
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159
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160
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161 @HELP_INPUT_DATA@
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162
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163
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164 Usage
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165 #####
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166 You can use csvtk to mutate a new column with data matched through regular expressions(regex).
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167
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168 A good Regular expressions cheat sheet that you can use to help yourself build regular expressions can be found at:
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169 https://regexr.com/
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170
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171 **Mutate Examples**
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172
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173 ::
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174
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175 Mutate with Filling empty columns when no regex match:
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176
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177 Suppose we have the following table and we want to pull out all of the exponent in the column "Colonies"
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178 without pulling out any of the other characters to make a new column called "Exponent":
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179
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180 +-------------+----------+-----------+
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181 | Colonies | Catalase | Coagulase |
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182 +=============+==========+===========+
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183 | 1x10^15 cfu | Yes | No |
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184 +-------------+----------+-----------+
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185 | 1x10^14 cfu | No | No |
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186 +-------------+----------+-----------+
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187 | 1x10^18 cfu | Yes | No |
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188 +-------------+----------+-----------+
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189 | 100 cfu | No | Yes |
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190 +-------------+----------+-----------+
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191
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192 We would use a Regex expression similar to (\^)(\d+) to get the "^" and the exponent into a new
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193 column giving the following result:
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194
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195 +-------------+----------+-----------+----------+
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196 | Colonies | Catalase | Coagulase | Exponent |
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197 +=============+==========+===========+==========+
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198 | 1x10^15 cfu | Yes | No | ^15 |
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199 +-------------+----------+-----------+----------+
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200 | 1x10^14 cfu | No | No | ^14 |
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201 +-------------+----------+-----------+----------+
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202 | 1x10^18 cfu | Yes | No | ^18 |
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203 +-------------+----------+-----------+----------+
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204 | 100 cfu | No | Yes | 100 cfu |
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205 +-------------+----------+-----------+----------+
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206
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207 As you can see we still have "100 cfu" at the bottom even though it doesn't contain a "^" as we
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208 did not specify that we wanted to make non-matches blank, we copied over the 100 cfu.
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209
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210 ----------------------------------------------------------------------------------------------------------------
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211
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212 Mutate leaving columns blank with no regex match:
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213
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214 Suppose we had the same chart as above:
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215
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216 +-------------+----------+-----------+
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217 | Colonies | Catalase | Coagulase |
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218 +=============+==========+===========+
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219 | 1x10^15 cfu | Yes | No |
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220 +-------------+----------+-----------+
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221 | 1x10^14 cfu | No | No |
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222 +-------------+----------+-----------+
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223 | 1x10^18 cfu | Yes | No |
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224 +-------------+----------+-----------+
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225 | 100 cfu | No | Yes |
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226 +-------------+----------+-----------+
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227
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228 Now, if we were to set "Fill Non-matches" to "No", then we would get the following table using the same inputs
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229 other than the change to fill non-matches:
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230
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231 +-------------+----------+-----------+----------+
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232 | Colonies | Catalase | Coagulase | Exponent |
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233 +=============+==========+===========+==========+
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234 | 1x10^15 cfu | Yes | No | ^15 |
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235 +-------------+----------+-----------+----------+
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236 | 1x10^14 cfu | No | No | ^14 |
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237 +-------------+----------+-----------+----------+
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238 | 1x10^18 cfu | Yes | No | ^18 |
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239 +-------------+----------+-----------+----------+
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240 | 100 cfu | No | Yes | |
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241 +-------------+----------+-----------+----------+
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242
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243 ----
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244
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245 If your having trouble with the regular expressions, please play around with a builder, there are many others online
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246 and they are great resources to improve your regex statements or test them before use!
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247
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248 ----
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249
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250 @HELP_END_STATEMENT@
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251
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252
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253 ]]></help>
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254 <expand macro="citations" />
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255 </tool>