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1 <tool id="cshl_find_and_replace" name="Find and Replace" version="0.1.1">
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2 <description>text</description>
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3 <command interpreter="perl">
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4 find_and_replace
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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 '$file_data'
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15 '$input1'
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16 </command>
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17 <inputs>
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18 <param format="txt" name="input1" type="data" label="File to process" />
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19
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20 <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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21 <sanitizer>
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22 <valid initial="string.printable">
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23 <remove value="'"/>
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24 </valid>
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25 </sanitizer>
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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 $& (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." >
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29 <sanitizer>
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30 <valid initial="string.printable">
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31 <remove value="'"/>
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32 </valid>
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33 </sanitizer>
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34 </param>
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35
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36 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Find-Pattern is a regular expression"
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37 help="see help section for details." />
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38
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39 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search"
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40 help="" />
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41
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42 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words"
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43 help="ignore partial matches (e.g. 'apple' will not match 'snapple') " />
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44
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45 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line"
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46 help="Select this option if the first line contains column headers. Text in the line will not be replaced. " />
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47
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48 <conditional name="searchwhere">
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49 <param name="choice" type="select" label="Replace text in">
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50 <option value="line" selected="true">entire line</option>
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51 <option value="column">specific column</option>
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52 </param>
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53
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54 <when value="line">
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55 </when>
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56
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57 <when value="column">
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58 <param name="column" label="in column" type="data_column" data_ref="input1" accept_default="true" />
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59 </when>
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60 </conditional>
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61 </inputs>
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62
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63 <outputs>
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64 <data format="input" name="output" metadata_source="input1"
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65 />
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66 </outputs>
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67
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68 <help>
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69
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70 **What it does**
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71
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72 This tool finds & replaces text in an input dataset.
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73
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74 .. class:: infomark
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75
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76 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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77
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78 .. class:: infomark
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79
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80 When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 )
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81
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82 .. class:: infomark
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83
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84 This tool uses Perl regular expression syntax.
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85
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86 -----
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87
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88 **Examples of *regular-expression* Find Patterns**
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89
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90 - **HELLO** The word 'HELLO' (case sensitive).
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91 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
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92 - **A{4,}** Four or more consecutive A's.
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93 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
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94 - **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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95
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96
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97 **Examples of Replace Patterns**
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98
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99 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
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100 - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&** (dollar-ampersand) represents the matched find pattern.
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101 - **$1** The text which matched the first parenthesis in the Find Pattern.
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102
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103
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104 -----
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105
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106 **Example 1**
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107
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108 **Find Pattern:** HELLO
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109 **Replace Pattern:** WORLD
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110 **Regular Expression:** no
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111 **Replace what:** entire line
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112
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113 Every time the word HELLO is found, it will be replaced with the word WORLD.
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114
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115 -----
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116
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117 **Example 2**
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118
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119 **Find Pattern:** ^chr
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120 **Replace Pattern:** (empty)
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121 **Regular Expression:** yes
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122 **Replace what:** column 11
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123
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124 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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125
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126
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127 -----
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128
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129 **Perl's Regular Expression Syntax**
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130
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131 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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132
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133 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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134 - **^** matches the beginning of a string(but not an internal line).
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135 - **(** .. **)** groups a particular pattern.
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136 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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137
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138 - **{n}** The preceding item is matched exactly n times.
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139 - **{n,}** The preceding item ismatched n or more times.
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140 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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141
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142 - **[** ... **]** 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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143 - **.** Matches any single character except a newline.
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144 - ***** The preceding item will be matched zero or more times.
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145 - **?** The preceding item is optional and matched at most once.
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146 - **+** The preceding item will be matched one or more times.
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147 - **^** has two meaning:
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148 - matches the beginning of a line or string.
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149 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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150 - **$** matches the end of a line or string.
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151 - **\\|** Separates alternate possibilities.
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152 - **\\d** matches a single digit
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153 - **\\w** matches a single letter or digit or an underscore.
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154 - **\\s** matches a single white-space (space or tabs).
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155
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156
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157 </help>
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158
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159 </tool>
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