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1 <tool id="cshl_find_and_replace" name="Find and Replace">
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2 <description>text</description>
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3 <command interpreter="perl">
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4 find_and_replace.pl
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5 #if $searchwhere.choice == "column":
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6 -c $searchwhere.column
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7 #end if
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8 -o $output
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9 $caseinsensitive
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10 $wholewords
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11 $skip_first_line
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12 $is_regex
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13 '$url_paste'
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14 '$file_data'
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15 '$input'
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16 </command>
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17 <inputs>
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18 <param format="txt" name="input" type="data" label="File to process" />
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19
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20 <!-- Note: the parameter ane MUST BE 'url_paste' -
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21 This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142)
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22 If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters
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23 will be passed to the shell script -->
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24 <param name="url_paste" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
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25 <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator>
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26 </param>
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27
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28 <param name="file_data" 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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29 <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator>
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30 </param>
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31
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32 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Find-Pattern is a regular expression"
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33 help="see help section for details." />
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34
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35 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search"
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36 help="" />
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37
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38 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words"
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39 help="ignore partial matches (e.g. 'apple' will not match 'snapple') " />
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40
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41 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line"
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42 help="Select this option if the first line contains column headers. Text in the line will not be replaced. " />
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43
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44 <conditional name="searchwhere">
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45 <param name="choice" type="select" label="Replace text in">
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46 <option value="line" selected="true">entire line</option>
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47 <option value="column">specific column</option>
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48 </param>
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49
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50 <when value="line">
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51 </when>
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52
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53 <when value="column">
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54 <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" />
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55 </when>
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56 </conditional>
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57 </inputs>
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58
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59 <outputs>
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60 <data format="input" name="output" metadata_source="input" />
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61 </outputs>
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62
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63 <help>
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64
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65 **What it does**
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66
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67 This tool finds & replaces text in an input dataset.
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68
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69 .. class:: infomark
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70
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71 The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box).
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72
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73 .. class:: infomark
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74
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75 When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 )
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76
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77 .. class:: infomark
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78
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79 This tool uses Perl regular expression syntax.
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80
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81 -----
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82
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83 **Examples of *regular-expression* Find Patterns**
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84
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85 - **HELLO** The word 'HELLO' (case sensitive).
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86 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
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87 - **A{4,}** Four or more consecutive A's.
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88 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
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89 - **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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90
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91
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92 **Examples of Replace Patterns**
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93
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94 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
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95 - **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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96 - **\\1** The text which matched the first parenthesis in the Find Pattern.
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97
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98
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99 -----
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100
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101 **Example 1**
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102
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103 **Find Pattern:** HELLO
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104 **Replace Pattern:** WORLD
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105 **Regular Expression:** no
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106 **Replace what:** entire line
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107
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108 Every time the word HELLO is found, it will be replaced with the word WORLD.
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109
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110 -----
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111
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112 **Example 2**
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113
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114 **Find Pattern:** ^chr
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115 **Replace Pattern:** (empty)
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116 **Regular Expression:** yes
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117 **Replace what:** column 11
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118
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119 If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet"
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120
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121
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122 -----
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123
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124 **Perl's Regular Expression Syntax**
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125
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126 The Find & Replace 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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127
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128 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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129 - **^** matches the beginning of a string(but not an internal line).
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130 - **(** .. **)** groups a particular pattern.
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131 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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132
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133 - **{n}** The preceding item is matched exactly n times.
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134 - **{n,}** The preceding item ismatched n or more times.
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135 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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136
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137 - **[** ... **]** 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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138 - **.** Matches any single character except a newline.
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139 - ***** The preceding item will be matched zero or more times.
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140 - **?** The preceding item is optional and matched at most once.
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141 - **+** The preceding item will be matched one or more times.
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142 - **^** has two meaning:
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143 - matches the beginning of a line or string.
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144 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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145 - **$** matches the end of a line or string.
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146 - **\\|** Separates alternate possibilities.
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147 - **\\d** matches a single digit
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148 - **\\w** matches a single letter or digit or an underscore.
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149 - **\\s** matches a single white-space (space or tabs).
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150
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151
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152 </help>
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153
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154 </tool>
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