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1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0">
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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="requirements">
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7 <requirement type="package" version="4.1.0">gnu_awk</requirement>
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8 </expand>
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9 <version_command>awk --version | head -n 1</version_command>
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10 <command interpreter="sh">
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11 <![CDATA[
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12 ##adapt to awk's quirks - to pass an acutal backslash - two backslashes are required (just like in a C string)
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13 REPLACE_PATTERN=\${$replace_pattern//\\/\\\\};
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14 awk
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15 -v OFS="\t"
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16 --re-interval
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17 --sandbox "{ \$$column = gensub( /$find_pattern/, \"$replace_pattern\", \"g\", \$$column ) ; print \$0 ; }"
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18 "$infile"
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19 > "$output"
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param format="tabular" name="infile" type="data" label="File to process" />
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24 <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />
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25
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26 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
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27 <sanitizer>
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28 <valid initial="string.printable">
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29 <remove value="'"/>
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30 </valid>
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31 </sanitizer>
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32 </param>
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33 <param name="replace_pattern" type="text" size="20" label="Replace with" help="Use simple text, or & (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
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34 <sanitizer>
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35 <valid initial="string.printable">
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36 <remove value="'"/>
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37 </valid>
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38 </sanitizer>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data format="input" name="output" metadata_source="infile" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="infile" value="replace_text_in_column_in1.txt" ftype="tabular" />
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47 <param name="column" value="4" />
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48 <param name="find_pattern" value=".+_(R.)" />
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49 <param name="replace_pattern" value="\1" />
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50 <output name="output" file="replace_text_in_column_output1.txt" />
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51 </test>
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52 </tests>
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53 <help>
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54 <![CDATA[
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55 **What it does**
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56
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57 This tool performs find & replace operation on a specified column in a given file.
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58
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59 .. class:: infomark
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60
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61 The **pattern to find** uses the **extended regular** expression syntax (same as running 'awk --re-interval').
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62
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63 .. class:: infomark
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64
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65 **TIP:** If you need more complex patterns, use the *awk* tool.
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66
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67 -----
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68
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69
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70 **Examples of Find Patterns**
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71
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72 - **HELLO** The word 'HELLO' (case sensitive).
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73 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
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74 - **A{4,}** Four or more consecutive A's.
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75 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
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76 - **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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77
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78
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79 **Examples of Replace Patterns**
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80
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81 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
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82 - **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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83 - **\\1** The text which matched the first parenthesis in the Find Pattern.
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84
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85
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86 -----
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87
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88 **Example 1**
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89
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90 **Find Pattern:** HELLO
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91 **Replace Pattern:** WORLD
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92
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93 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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94
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95 -----
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96
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97 **Example 2**
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98
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99 **Find Pattern:** ^(.{4})
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100 **Replace Pattern:** &\\t
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101
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102 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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103
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104
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105 -----
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106
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107 **Extened Regular Expression Syntax**
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108
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109 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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110
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111 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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112 - **^** matches the beginning of a string(but not an internal line).
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113 - **(** .. **)** groups a particular pattern.
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114 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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115
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116 - **{n}** The preceding item is matched exactly n times.
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117 - **{n,}** The preceding item ismatched n or more times.
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118 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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119
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120 - **[** ... **]** 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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121 - **.** Matches any single character except a newline.
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122 - ***** The preceding item will be matched zero or more times.
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123 - **?** The preceding item is optional and matched at most once.
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124 - **+** The preceding item will be matched one or more times.
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125 - **^** has two meaning:
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126 - matches the beginning of a line or string.
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127 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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128 - **$** matches the end of a line or string.
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129 - **\|** Separates alternate possibilities.
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130
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131
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132 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
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133
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134 @REFERENCES@
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135 ]]>
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136 </help>
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137 </tool>
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