Mercurial > repos > galaxyp > regex_find_replace

annotate regex_tabular.xml @ 5:96eb105e71d8 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 3eaa2a2bdaeedf1b0771b1b764a550106dcbc186
author galaxyp
date Thu, 02 Feb 2023 08:21:21 +0000
parents d72a404cef12
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
96eb105e71d8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 3eaa2a2bdaeedf1b0771b1b764a550106dcbc186
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1 <tool id="regexColumn1" name="Column Regex Find And Replace" version="1.0.3" profile="21.01">
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>
6dcfb96bc8b0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 8871a847daed1f996c0a2069c3e876685bf8d220"
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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 --column $field
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11 --input_display_name '$input.display_name'
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12 #for $check in $checks:
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13 --pattern='$check.pattern' --replacement='$check.replacement'
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14 #end for
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15 </command>
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16 <inputs>
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17 <param format="tabular" name="input" type="data" label="Select cells from"/>
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18 <param name="field" label="using column" type="data_column" data_ref="input" />
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19 <repeat name="checks" title="Check">
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20 <param name="pattern" 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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21 <sanitizer>
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22 <valid>
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23 <add preset="string.printable"/>
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24 <remove value="&#92;" />
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25 <remove value="&apos;" />
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26 </valid>
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27 <mapping initial="none">
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28 <add source="&#92;" target="__backslash__" />
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29 <add source="&apos;" target="__sq__"/>
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30 </mapping>
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31 </sanitizer>
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32 </param>
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33 <param name="replacement" type="text" value="newchr\1" label="Replacement">
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34 <sanitizer>
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35 <valid>
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36 <add preset="string.printable"/>
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37 <remove value="&#92;" />
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38 <remove value="&apos;" />
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39 </valid>
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40 <mapping initial="none">
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41 <add source="&#92;" target="__backslash__" />
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42 <add source="&apos;" target="__sq__"/>
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43 </mapping>
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44 </sanitizer>
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45 </param>
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46 </repeat>
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47 </inputs>
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48 <outputs>
5
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49 <data format_source="input" name="out_file1" metadata_source="input" />
0
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="input" value="find_tabular_1.txt" ftype="tabular" />
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54 <param name="field" value="2" />
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55 <param name="pattern" value="moo"/>
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56 <param name="replacement" value="cow" />
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57 <output name="out_file1" file="replace_tabular_1.txt" ftype="tabular"/>
0
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58 </test>
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59 <test>
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60 <param name="input" value="find_tabular_1.txt" ftype="tabular" />
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61 <param name="field" value="1" />
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62 <param name="pattern" value="moo"/>
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63 <param name="replacement" value="cow" />
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64 <output name="out_file1" file="replace_tabular_2.txt" ftype="tabular"/>
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65 </test>
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66 </tests>
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67 <help>
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68
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69 .. class:: warningmark
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70
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71 **This tool will attempt to reuse the metadata from your first input.** To change metadata assignments click on the "edit attributes" link of the history item generated by this tool.
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72
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73 .. class:: infomark
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74
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75 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
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76
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77 -----
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78
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79 This tool goes line by line through the specified input file and
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80 if the text in the selected column matches a specified regular expression pattern
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81 replaces the text with the corresponding specified replacement.
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82
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83 This tool can be used to change between the chromosome naming conventions of UCSC and Ensembl.
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84
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85 For example to remove the **chr** part of the reference sequence name in the first column of this GFF file::
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86
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87 ##gff-version 2
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88 ##Date: Thu Mar 23 11:21:17 2006
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89 ##bed2gff.pl $Rev: 601 $
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90 ##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
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91 chr1 bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f 148325916 148325975 . + . score "0";
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92 chr21 bed2gff CCDS13614.1_cds_0_0_chr21_32707033_f 32707033 32707192 . + . score "0";
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93 chrX bed2gff CCDS14606.1_cds_0_0_chrX_122745048_f 122745048 122745924 . + . score "0";
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94
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95 Setting::
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96
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97 using column: c1
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98 Find Regex: chr([0-9]+|X|Y|M[Tt]?)
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99 Replacement: \1
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100
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101 produces::
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102
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103 ##gff-version 2
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104 ##Date: Thu Mar 23 11:21:17 2006
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105 ##bed2gff.pl $Rev: 601 $
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106 ##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
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107 1 bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f 148325916 148325975 . + . score "0";
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108 21 bed2gff CCDS13614.1_cds_0_0_chr21_32707033_f 32707033 32707192 . + . score "0";
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109 X bed2gff CCDS14606.1_cds_0_0_chrX_122745048_f 122745048 122745924 . + . score "0";
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110
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111
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112 This tool uses Python regular expressions with the **re.sub()** function.
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113 More information about Python regular expressions can be found here:
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114 http://docs.python.org/library/re.html.
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115
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116 The regex **chr([0-9]+|X|Y|M)** means start with text **chr** followed by either: one or more digits, or the letter X, or the letter Y, or the letter M (optionally followed by a single letter T or t).
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117 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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118
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119
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120 In the replacement pattern, use the special token #{input_name} to insert the input dataset's display name.
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121 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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122 named **Sample ABC123**, into the dataset itself, which currently contains the lines::
1
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123
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124 Data 1
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125 Data 2
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126 Data 3
0
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127
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128 You can use the following checks::
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129
1
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130 Find Regex: Data
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131 Replacement: #{input_name} Data
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132
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133 Find Regex: Sample (\S+)
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134 Replacement: \1
0
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135
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136 The result will be::
1
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137
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138 ABC123 Data 1
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139 ABC123 Data 2
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140 ABC123 Data 3
0
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141
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142
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143
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144 Galaxy aggressively escapes input supplied to tools, so if something
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145 is not working please let us know and we can look into whether this is
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146 the cause. Also if you would like help constructing regular
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147 expressions for your inputs, please let us know at help@msi.umn.edu.
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148
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149 </help>
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150 </tool>