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1 <tool id="regex_replace" name="Regex Replace" version="1.0.0">
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2 <description>Regular Expression replacement using the Python re module</description>
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3 <command interpreter="python">$script_file</command>
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4 <inputs>
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5 <param name="infile" type="data" label="Input File"/>
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6 <param name="search_str" type="text" size="70" label="Search String">
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7 <sanitizer>
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8 <valid initial="string.printable">
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9 <remove value="""/>
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10 <remove value="\"/>
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11 </valid>
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12 <mapping initial="none">
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13 <add source=""" target="\""/>
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14 <add source="\" target="\\"/>
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15 </mapping>
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16 </sanitizer>
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17 </param>
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18 <param name="replace_str" type="text" size="70" label="Replace String">
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19 <sanitizer>
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20 <valid initial="string.printable">
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21 <remove value="""/>
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22 <remove value="\"/>
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23 </valid>
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24 <mapping initial="none">
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25 <add source=""" target="\""/>
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26 <add source="\" target="\\"/>
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27 </mapping>
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28 </sanitizer>
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29 </param>
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30 <param name="multiline" type="boolean" label="Multi-line" checked="False"/>
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31 <param name="ignore_case" type="boolean" label="Ignore Case" checked="False"/>
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32 <param name="dot_all" type="boolean" label="Dot All" checked="False"/>
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33 <param name="replace_count" type="integer" label="Replace Count(0=all)" value="0"/>
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34 </inputs>
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35 <outputs>
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36 <data name="outfile" format="txt"/>
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37 </outputs>
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38 <configfiles>
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39 <configfile name="script_file"><![CDATA[#!/usr/bin/env python
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40
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41 import re
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42
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43 search_str = """${search_str}"""
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44 replace_str = """${replace_str}"""
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45
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46 opts = 0
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47 #if $ignore_case:
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48 opts |= re.IGNORECASE
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49 #end if
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50 #if $multiline:
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51 opts |= re.MULTILINE
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52 #end if
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53 #if $dot_all:
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54 opts |= re.DOTALL
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55 #end if
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56 cmd = re.compile(search_str, opts)
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57
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58 ihandle = open("""${infile}""")
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59 ohandle = open("""${outfile}""", "w")
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60
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61 #if $multiline:
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62 itext = ihandle.read()
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63 otext = cmd.sub(replace_str, itext, count=$replace_count )
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64 ohandle.write(otext)
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65 #else
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66 for line in ihandle:
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67 oline = cmd.sub(replace_str, line, count=$replace_count )
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68 ohandle.write(oline)
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69 #end if
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70
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71 ihandle.close()
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72 ohandle.close()
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73
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74 ]]></configfile>
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75 </configfiles>
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76
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77 <help>
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78 Perform regular expression replacement using the Python re engine.
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79
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80 Example:
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81 ========
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82 Search String::
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83
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84 [^\s]+_(\w+).*
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85
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86 Replace String::
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87
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88 \1
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89
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90 On the input file::
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91
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92 LJP001_BT20_24H:DMSO
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93 LJP001_BT20_24H:H20
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94 LJP001_BT20_6H:DMSO
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95
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96 Outputs::
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97
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98 24H
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99 24H
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100 6H
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101
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102 Additional Options
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103 ==================
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104
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105 Replace Count:
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106 Will define the number of occurrences that can be replaced by the substitution. A count of 0 is equivalent
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107 to 'replace all'
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108
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109
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110 Ignore Case:
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111 Make searches case insensitive
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112
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113 Multi-line:
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114 Do the search across the entire contents of the file. If not checked, then replacements occur line by line
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115
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116 Dot-All:
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117 With this checked, the '.' in a matching pattern will also match new-line characters. Generally used with 'multi-line' search
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118
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119 </help>
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120 </tool>
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