Mercurial > repos > galaxyp > regex_find_replace

annotate regex.xml @ 3:ae8c4b2488e7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 0595f14f3b95f8b8190b58625217c72e76c649ee"
author galaxyp
date Fri, 08 May 2020 04:01:27 -0400
parents 538933d9fccc
children 399da6b5ec21
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538933d9fccc "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 8871a847daed1f996c0a2069c3e876685bf8d220"
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1 <tool id="regex1" name="Regex Find And Replace" version="1.0.1">
0
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2 <description></description>
2
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
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5 </requirements>
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6 <command>
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7 python '$__tool_directory__/regex.py'
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8 --input '$input'
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9 --output '$out_file1'
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10 --input_display_name '$input.display_name'
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11 #for $check in $checks:
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12 --pattern='$check.pattern' --replacement='$check.replacement'
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13 #end for
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14 </command>
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15 <inputs>
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16 <param format="txt" name="input" type="data" label="Select lines from"/>
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17 <repeat name="checks" title="Check">
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18 <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)">
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19 <sanitizer>
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20 <valid>
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21 <add preset="string.printable"/>
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22 <remove value="&#92;" />
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23 <remove value="&apos;" />
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24 </valid>
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25 <mapping initial="none">
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26 <add source="&#92;" target="__backslash__" />
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27 <add source="&apos;" target="__sq__"/>
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28 </mapping>
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29 </sanitizer>
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30 </param>
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31 <param name="replacement" size="40" type="text" value="newchr\1" label="Replacement">
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32 <sanitizer>
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33 <valid>
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34 <add preset="string.printable"/>
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35 <remove value="&#92;" />
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36 <remove value="&apos;" />
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37 </valid>
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38 <mapping initial="none">
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39 <add source="&#92;" target="__backslash__" />
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40 <add source="&apos;" target="__sq__"/>
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41 </mapping>
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42 </sanitizer>
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43 </param>
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44 </repeat>
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45 </inputs>
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46 <outputs>
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47 <data format="input" name="out_file1" metadata_source="input"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="input" value="find1.txt"/>
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52 <param name="pattern" value="(T\w+)"/>
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53 <param name="replacement" value="\1 \1" />
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54 <output name="out_file1" file="replace1.txt"/>
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55 </test>
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56 <test>
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57 <param name="input" value="find1.txt"/>
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58 <param name="pattern" value="f"/>
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59 <param name="replacement" value="'&quot;" />
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60 <output name="out_file1" file="replace2.txt"/>
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61 </test>
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62 <test>
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63 <param name="input" value="find1.txt"/>
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64 <param name="checks_0|pattern" value="a test file"/>
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65 <param name="checks_0|replacement" value="a file named #{input_name}" />
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66 <param name="checks_1|pattern" value="see here"/>
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67 <param name="checks_1|replacement" value="see #{input_name}" />
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68 <param name="checks_2|pattern" value="see (find1).txt"/>
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69 <param name="checks_2|replacement" value="see \1" />
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70 <output name="out_file1" file="replace3.txt"/>
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71 </test>
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72 </tests>
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73 <help>
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74 This tool goes line by line through the specified input file and
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75 replaces text which matches the specified regular expression patterns
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76 with its corresponding specified replacement.
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77
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78 This tool uses Python regular expressions. More information about
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79 Python regular expressions can be found here:
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80 http://docs.python.org/library/re.html.
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81
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82 To convert an Ilumina FATSQ sequence id from the CAVASA 8 format::
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83
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84 @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
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85 GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
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86 +EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
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87 IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
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88
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89 To the CASAVA 7 format::
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90
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91 @EAS139_FC706VJ:2:2104:15343:197393#0/1
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92 GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
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93 +EAS139_FC706VJ:2:2104:15343:197393#0/1
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94 IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
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95
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96 Use Settings::
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97
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98 Find Regex: ^([@+][A-Z0-9]+):\d+:(\S+)\s(\d).*$
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99 Replacement: \1_\2#0/\3
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100
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101 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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102
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103 The regex **^([@+][A-Z0-9]+):\d+:(\S+) (\d).*$** means::
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104
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105 ^ - start the match at the beginning of the line of text
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106 ( - 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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107 [@+] - matches either a @ or + character
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108 [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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109 ) - 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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110 :\d+: - matches a colon followed by one or more digits followed by a colon character
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111 (\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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112 \s - matches a whitespace character
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113 (\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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114 .* - dot means match any character, asterisk means zero more more matches
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115 $ - the regex must match to the end of the line of text
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116
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117 In the replacement pattern, use the special token #{input_name} to insert the input dataset's display name.
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118 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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119 named **Sample ABC123**, into the dataset itself, which currently contains the lines::
1
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120
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121 Data 1
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122 Data 2
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123 Data 3
0
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124
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125 You can use the following checks::
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126
1
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127 Find Regex: Data
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128 Replacement: #{input_name} Data
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129
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130 Find Regex: Sample (\S+)
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131 Replacement: \1
0
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132
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133 The result will be::
1
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134
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135 ABC123 Data 1
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136 ABC123 Data 2
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137 ABC123 Data 3
0
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138
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139
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140
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141 Galaxy aggressively escapes input supplied to tools, so if something
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142 is not working please let us know and we can look into whether this is
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143 the cause. Also if you would like help constructing regular
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144 expressions for your inputs, please let us know at help@msi.umn.edu.
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145 </help>
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146 </tool>