Mercurial > repos > nml > csvtk_replace
annotate replace.xml @ 0:1d4ee4308d99 draft default tip
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author | nml |
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date | Tue, 19 May 2020 17:16:05 -0400 |
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0
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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1 <tool id="csvtk_replace" name="csvtk-replace" version="@VERSION@+@GALAXY_VERSION@"> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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2 <description> data of selected columns by regular expression</description> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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3 <macros> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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4 <import>macros.xml</import> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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5 </macros> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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6 <expand macro="requirements" /> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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7 <expand macro="version_cmd" /> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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8 <command detect_errors="exit_code"><![CDATA[ |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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9 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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10 ################### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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11 ## Start Command ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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12 ################### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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13 csvtk replace --num-cpus "\${GALAXY_SLOTS:-1}" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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14 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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15 ## Add additional flags as specified ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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16 ####################################### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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17 $ignore_case |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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18 $global_param.illegal_rows |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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19 $global_param.empty_rows |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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20 $global_param.header |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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21 $global_param.lazy_quotes |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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22 |
1d4ee4308d99
"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 ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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24 ############################################################# |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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25 #if $in_1.is_of_type("tabular"): |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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26 -t -T |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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27 #end if |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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28 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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29 ## Set input files ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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30 ##################### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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31 '$in_1' |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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32 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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33 ## Specify fields to use ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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34 ########################### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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35 -F -f '${column_text.in_text}' |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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36 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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37 ## Specific Commands ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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38 ####################### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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39 -p '($pattern_string)' |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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40 -r '$replacement_string' |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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41 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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42 #if $input_kv |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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43 -k '$input_kv' |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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44 #end if |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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45 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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46 #if $fill.how_fill == "key" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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47 -K |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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48 #elif $fill.how_fill == "string" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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49 --key-miss-repl '$fill.fill_string' |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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50 #end if |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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51 |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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52 ## To output ## |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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53 ############### |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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54 > replaced |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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55 |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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56 ]]></command> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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57 <inputs> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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58 <expand macro="singular_input"/> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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59 <expand macro="fields_input" /> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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60 <param name="pattern_string" type="text" argument="-p" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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61 label="Pattern Regex" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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62 help="Regex to search column for. Input is structured as '(YOUR_INPUT_HERE)' so if your regex was just a period it would look like '(.)' as an input."> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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63 <expand macro="text_sanitizer" /> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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64 </param> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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65 <param name="replacement_string" type="text" argument="-r" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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66 label="Replacement String"> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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67 <help> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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68 <![CDATA[ |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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69 String to replace found data. Supports capture variables and special replacement symbols. |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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70 |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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71 - Capture Variables: $1 represents the text of the first submatch |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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72 - {nr} inserts a record number starting from 1 |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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73 - {kv} uses corresponding value of the key (captured variable $n) of a key-value file |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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74 |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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75 If using the special replacement symbols, the capture variable must be specified as ${1}! |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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76 ]]> |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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77 </help> |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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78 <expand macro="text_sanitizer" /> |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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79 </param> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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80 <param name="input_kv" type="data" format="tsv,tabular" argument="-k" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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81 optional="true" |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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82 label="Key/Value file for replacement string" |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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83 help="Only specify a file if using {kv} in replacement string. The file must be tab delimited with one key/value pair per line. |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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84 An example can be found in the help section below" |
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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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85 /> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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86 <conditional name="fill"> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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87 <param name="how_fill" type="select" label="Fill columns that don't get any regex matches"> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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88 <option value="no">No</option> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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89 <option value="key">Yes - Fill with Original Value</option> |
1d4ee4308d99
"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
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90 <option value="string">Yes - Fill with String</option> |
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91 </param> |
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92 <when value="no" /> |
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93 <when value="key" /> |
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94 <when value="string" > |
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95 <param name="fill_string" type="text" value="NA" argument="--key-miss-repl" label="Fill string"> |
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96 <expand macro="text_sanitizer" /> |
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97 </param> |
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98 </when> |
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99 </conditional> |
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100 <expand macro="ignore_case" /> |
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101 <expand macro="global_parameters" /> |
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102 </inputs> |
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103 <outputs> |
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104 <data format_source="in_1" name="replaced" from_work_dir="replaced" label='${in_1.name} with column ${column_text.in_text} replaced' /> |
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105 </outputs> |
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106 <tests> |
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107 <test> |
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108 <param name="in_1" value="replace_input.csv" /> |
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109 <conditional name="column_text"> |
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110 <param name="select" value="string" /> |
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111 <param name="in_text" value="2" /> |
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112 </conditional> |
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113 <param name="pattern_string" value=".+" /> |
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114 <param name="replacement_string" value="{nr}-$1" /> |
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115 <output name="replaced" value="replace_1.csv" /> |
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116 </test> |
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117 <test> |
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118 <param name="in_1" value="replace_input.csv" /> |
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119 <conditional name="column_text"> |
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120 <param name="select" value="string" /> |
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121 <param name="in_text" value="2" /> |
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122 </conditional> |
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123 <param name="pattern_string" value=".+" /> |
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124 <param name="replacement_string" value="{kv}" /> |
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125 <param name="input_kv" value="kv.txt" /> |
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126 <conditional name="fill"> |
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127 <param name="how_fill" value="key" /> |
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128 </conditional> |
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129 <output name="replaced" value="replace_2.csv" /> |
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130 </test> |
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131 </tests> |
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132 <help><![CDATA[ |
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133 |
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134 Csvtk - Replace Help |
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135 -------------------- |
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136 |
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137 Info |
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138 #### |
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139 Csvtk-replace is a tool that uses Regular Expressions (Regex) to match data in the specified column and replace it with the replacement string. |
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140 Non-matched columns can be kept or filled with the Regex key or an input string |
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141 |
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142 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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143 start your expression with a `^` or just go straight into it |
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144 |
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145 For example: |
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146 |
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147 :: |
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148 |
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149 Using `.+` as an input would be used in the code as '(.+)' |
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150 |
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151 Using ^(.+)$ as an input would yield an input in the code as '(^(.+)$)' |
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152 |
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153 .. class:: warningmark |
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154 |
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155 Single quotes are not allowed in text inputs! |
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156 |
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157 ----- |
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158 |
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159 |
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160 @HELP_INPUT_DATA@ |
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161 |
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162 |
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163 Usage |
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164 ##### |
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165 You can use csvtk replace to any matched regex expressions with your input replacement string. |
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166 |
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167 The replacement string has some unique properties that you can use too to better replace your data: |
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168 |
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169 - Replacement supports capture variables, like $1 which represents the text of the first submatch of the Regex |
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170 |
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171 - \{nr} can be used to assign ascending numbers starting from 1 to each column |
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172 |
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173 - \{kv} can be used to get the value of the key (captured variable $n) or a key-value file |
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174 |
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175 A good Regular expressions cheat sheet that you can use to help yourself build regular expressions can be found at: |
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176 https://regexr.com/ |
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177 |
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178 **Replace Examples** |
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179 |
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180 1. Replacement with {nr} and $1 |
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181 |
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182 Input file: |
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183 |
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184 +---------+--------+ |
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185 | Name | Animal | |
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186 +=========+========+ |
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187 | Bud | Dog | |
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188 +---------+--------+ |
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189 | Mittens | Cat | |
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190 +---------+--------+ |
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191 |
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192 Now if our regex was set to '.*' on column 2 and our replacement string was set to '{nr}-$1', the following output would be observed: |
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193 |
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194 +---------+--------+ |
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195 | Name | Animal | |
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196 +=========+========+ |
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197 | Bud | 1-Dog | |
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198 +---------+--------+ |
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199 | Mittens | 2-Cat | |
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200 +---------+--------+ |
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201 |
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202 --------------- |
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203 |
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204 2. Replacement with {kv} file |
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205 |
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206 Suppose you set up a key-value TAB separated file that looked as such: |
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207 |
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208 :: |
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209 |
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210 Key Value |
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211 Dog Big |
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212 Cat Small |
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213 |
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214 And had a similar input file: |
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215 |
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216 +---------+--------+ |
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217 | Name | Animal | |
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218 +=========+========+ |
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219 | Bud | Dog | |
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220 +---------+--------+ |
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221 | Mittens | Cat | |
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222 +---------+--------+ |
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223 | Fuzzy | Gerbil | |
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224 +---------+--------+ |
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225 |
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226 Now if the regex was '.*' on column 2 with the replacement string as '{kv}'. Your output would look as such with 'No' fill specified: |
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227 |
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228 +---------+--------+ |
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229 | Name | Animal | |
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230 +=========+========+ |
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231 | Bud | Big | |
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232 +---------+--------+ |
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233 | Mittens | Small | |
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234 +---------+--------+ |
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235 | Fuzzy | | |
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236 +---------+--------+ |
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237 |
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238 If you wanted to fill the blank cell you could set it to either: |
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239 |
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240 - String - the string you input (ex. 'NA') would fill up the blank cell. |
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241 |
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242 - Original value - would change the blank cell to 'Gerbil' |
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243 |
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244 ---- |
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245 |
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246 If your having trouble with the regular expressions, please play around with a builder, there are many others online |
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247 and they are great resources to improve your regex statements or test them before use! |
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248 |
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249 ---- |
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250 |
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251 @HELP_END_STATEMENT@ |
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252 |
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253 |
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254 ]]></help> |
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255 <expand macro="citations" /> |
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256 </tool> |