Mercurial > repos > bgruening > text_processing

annotate replace_text_in_column.xml @ 23:6073bb457ec0 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 7cdafed6c6a1387395e5a869186518f129aa3132
author bgruening
date Tue, 25 Mar 2025 14:34:17 +0000
parents 3dc70b59608c
children
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1 <tool id="tp_replace_in_column" name="Replace Text" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>in a specific column</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="creator"/>
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7 <requirements>
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8 <requirement type="package" version="5.3.1">gawk</requirement>
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9 </requirements>
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10 <version_command>awk --version | head -n 1</version_command>
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11 <command>
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12 <![CDATA[
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13 awk
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14 -v OFS="\t"
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15 -v FS="\t"
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16 --re-interval
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17 --sandbox
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18 '{
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19 #for $replacement in $replacements:
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20 \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ;
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21 #end for
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22 print \$0 ; }'
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23 '$infile'
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24 > '$outfile'
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param format="tabular" name="infile" type="data" label="File to process" />
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29 <repeat name="replacements" title="Replacement" min="1">
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30 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
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31
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32 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
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33 <sanitizer>
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34 <valid initial="string.printable">
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35 <remove value="&apos;"/>
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36 </valid>
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37 </sanitizer>
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38 </param>
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39 <param name="replace_pattern" type="text" label="Replace with" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="&apos;"/>
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43 </valid>
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44 </sanitizer>
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45 </param>
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46 </repeat>
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47 </inputs>
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48 <outputs>
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49 <data name="outfile" format_source="infile" metadata_source="infile" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
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54 <repeat name="replacements">
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55 <param name="column" value="4" />
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56 <param name="find_pattern" value=".+_(R.)" />
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57 <param name="replace_pattern" value="\\1" />
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58 </repeat>
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59 <output name="outfile" file="replace_text_in_column_results1.txt" />
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60 </test>
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61 <test>
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62 <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
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63 <repeat name="replacements">
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64 <param name="column" value="1" />
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65 <param name="find_pattern" value="[a-z]{2}([a-z])" />
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66 <param name="replace_pattern" value="\\1" />
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67 </repeat>
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68 <repeat name="replacements">
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69 <param name="column" value="4" />
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70 <param name="find_pattern" value=".+_(R.)" />
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71 <param name="replace_pattern" value="\\1" />
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72 </repeat>
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73 <output name="outfile" file="replace_text_in_column_results2.txt" />
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74 </test>
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75 </tests>
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76 <help>
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77 <![CDATA[
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78 **What it does**
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79
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80 This tool performs find & replace operation on a specified column in a given file.
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81
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82 .. class:: infomark
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83
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84 The **pattern to find** uses the **extended regular** expression syntax (same as running 'awk --re-interval').
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85
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86 .. class:: infomark
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87
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88 **TIP:** If you need more complex patterns, use the *awk* tool.
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89
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90 -----
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91
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92
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93 **Examples of Find Patterns**
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94
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95 - **HELLO** The word 'HELLO' (case sensitive).
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96 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
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97 - **A{4,}** Four or more consecutive A's.
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98 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
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99 - **hsa-mir-([^ ]+)** The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.
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100
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101
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102 **Examples of Replace Patterns**
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103
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104 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
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105 - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&** (ampersand) represents the matched find pattern.
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106 - **\\1** The text which matched the first parenthesis in the Find Pattern.
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107
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108
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109 -----
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110
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111 **Example 1**
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112
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113 **Find Pattern:** HELLO
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114 **Replace Pattern:** WORLD
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115
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116 Every time the word HELLO is found, it will be replaced with the word WORLD. This operation affects only the selected column.
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117
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118 -----
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119
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120 **Example 2**
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121
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122 **Find Pattern:** ^(.{4})
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123 **Replace Pattern:** &\\t
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124
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125 Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns. This operation affects only the selected column.
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126
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127
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128 -----
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129
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130 **Extened Regular Expression Syntax**
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131
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132 The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.
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133
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134 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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135 - **^** matches the beginning of a string(but not an internal line).
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136 - **(** .. **)** groups a particular pattern.
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137 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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138
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139 - **{n}** The preceding item is matched exactly n times.
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140 - **{n,}** The preceding item ismatched n or more times.
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141 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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142
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143 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
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144 - **.** Matches any single character except a newline.
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145 - ***** The preceding item will be matched zero or more times.
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146 - **?** The preceding item is optional and matched at most once.
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147 - **+** The preceding item will be matched one or more times.
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148 - **^** has two meaning:
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149 - matches the beginning of a line or string.
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150 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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151 - **$** matches the end of a line or string.
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152 - **\|** Separates alternate possibilities.
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153
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154
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155 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
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156
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157 ]]>
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158 </help>
6
60edf2f8c28f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
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159 <expand macro="citations" />
0
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160 </tool>