Mercurial > repos > galaxyp > regex_find_replace

annotate regex.xml @ 0:002f95cf9d6e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
author galaxyp
date Wed, 18 Jan 2017 17:45:06 -0500
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children bf0c0905fd60
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
galaxyp
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1 <tool id="regex1" name="Regex Find And Replace" version="1.0.0">
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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2 <description></description>
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3 <command interpreter="python">regex.py --input '$input' --output '$out_file1' --input_display_name '$input.display_name'
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
galaxyp
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4 #for $check in $checks:
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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5 --pattern='$check.pattern' --replacement='$check.replacement'
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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6 #end for
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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7 </command>
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galaxyp
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8 <inputs>
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galaxyp
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9 <param format="txt" name="input" type="data" label="Select lines from"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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10 <repeat name="checks" title="Check">
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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11 <param name="pattern" size="40" type="text" value="chr([0-9A-Za-z])+" label="Find Regex" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
galaxyp
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12 <sanitizer>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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13 <valid>
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14 <add preset="string.printable"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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15 <remove value="&#92;" />
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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16 <remove value="&apos;" />
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17 </valid>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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18 <mapping initial="none">
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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19 <add source="&#92;" target="__backslash__" />
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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20 <add source="&apos;" target="__sq__"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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21 </mapping>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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22 </sanitizer>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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23 </param>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
galaxyp
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24 <param name="replacement" size="40" type="text" value="newchr\1" label="Replacement">
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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25 <sanitizer>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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26 <valid>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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27 <add preset="string.printable"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
galaxyp
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28 <remove value="&#92;" />
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
galaxyp
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29 <remove value="&apos;" />
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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30 </valid>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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31 <mapping initial="none">
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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32 <add source="&#92;" target="__backslash__" />
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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33 <add source="&apos;" target="__sq__"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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34 </mapping>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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35 </sanitizer>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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36 </param>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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37 </repeat>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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38 </inputs>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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39 <outputs>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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40 <data format="input" name="out_file1" metadata_source="input"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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41 </outputs>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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42 <tests>
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43 <test>
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44 <param name="input" value="find1.txt"/>
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45 <param name="pattern" value="(T\w+)"/>
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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46 <param name="replacement" value="\1 \1" />
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47 <output name="out_file1" file="replace1.txt"/>
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48 </test>
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49 <test>
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50 <param name="input" value="find1.txt"/>
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51 <param name="pattern" value="f"/>
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52 <param name="replacement" value="'&quot;" />
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53 <output name="out_file1" file="replace2.txt"/>
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54 </test>
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55 <test>
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56 <param name="input" value="find1.txt"/>
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57 <param name="checks_0|pattern" value="a test file"/>
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58 <param name="checks_0|replacement" value="a file named #{input_name}" />
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59 <param name="checks_1|pattern" value="see here"/>
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60 <param name="checks_1|replacement" value="see #{input_name}" />
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61 <param name="checks_2|pattern" value="see (find1).txt"/>
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62 <param name="checks_2|replacement" value="see \1" />
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63 <output name="out_file1" file="replace3.txt"/>
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64 </test>
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65 </tests>
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66 <help>
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67 This tool goes line by line through the specified input file and
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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68 replaces text which matches the specified regular expression patterns
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69 with its corresponding specified replacement.
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70
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71 This tool uses Python regular expressions. More information about
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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72 Python regular expressions can be found here:
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73 http://docs.python.org/library/re.html.
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74
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75 To convert an Ilumina FATSQ sequence id from the CAVASA 8 format::
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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76
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77 @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
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78 GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
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79 +EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
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80 IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
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81
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82 To the CASAVA 7 format::
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83
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84 @EAS139_FC706VJ:2:2104:15343:197393#0/1
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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85 GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
002f95cf9d6e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 568a615b191482c54ecb31399ba27f78d6c71510
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86 +EAS139_FC706VJ:2:2104:15343:197393#0/1
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87 IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
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88
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89 Use Settings::
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90
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91 Find Regex: ^([@+][A-Z0-9]+):\d+:(\S+)\s(\d).*$
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92 Replacement: \1_\2#0/\3
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93
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94 Note that the parentheses **()** capture patterns in the text that can be used in the replacement text by using a backslash-number reference: **\\1**
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95
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96 The regex **^([@+][A-Z0-9]+):\d+:(\S+) (\d).*$** means::
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97
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98 ^ - start the match at the beginning of the line of text
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99 ( - start a group (1), that is a string of matched text, that can be back-referenced in the replacement as \1
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100 [@+] - matches either a @ or + character
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101 [A-Z0-9]+ - matches an uppercase letter or a digit, the plus sign means to match 1 or more such characters
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102 ) - end a group (1), that is a string of matched text, that can be back-referenced in the replacement as \1
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103 :\d+: - matches a colon followed by one or more digits followed by a colon character
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104 (\S+) - matches one or more non-whitespace charcters, the enclosing parentheses make this a group (2) that can back-referenced in the replacement text as \2
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105 \s - matches a whitespace character
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106 (\d) - matches a single digit character, the enclosing parentheses make this a group (3) that can back-referenced in the replacement text as \3
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107 .* - dot means match any character, asterisk means zero more more matches
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108 $ - the regex must match to the end of the line of text
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109
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110 In the replacement pattern, use the special token #{input_name} to insert the input dataset's display name.
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111 The name can be modified by a second find/replace check. Suppose you want to insert the sample id of your dataset,
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112 named **Sample ABC123**, into the dataset itself, which currently contains the lines::
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113 Data 1
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114 Data 2
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115 Data 3
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116
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117 You can use the following checks::
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118 Find Regex: Data
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119 Replacement: #{input_name} Data
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120
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121 Find Regex: Sample (\S+)
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122 Replacement: \1
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123
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124 The result will be::
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125 ABC123 Data 1
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126 ABC123 Data 2
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127 ABC123 Data 3
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128
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129
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130
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131 Galaxy aggressively escapes input supplied to tools, so if something
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132 is not working please let us know and we can look into whether this is
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133 the cause. Also if you would like help constructing regular
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134 expressions for your inputs, please let us know at help@msi.umn.edu.
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135 </help>
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136 </tool>