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comparison regex_tabular.xml @ 0:9ea374bb0350 draft default tip

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author jjohnson
date Sat, 29 Mar 2014 13:41:51 -0400
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1 <tool id="regexColumn1" name="Column Regex Find And Replace" version="0.1.0">
2 <description></description>
3 <command interpreter="python">regex.py --input $input --output $out_file1 --column $field
4 #for $check in $checks:
5 --pattern='$check.pattern' --replacement='$check.replacement'
6 #end for
7 </command>
8 <inputs>
9 <param format="tabular" name="input" type="data" label="Select cells from"/>
10 <param name="field" label="using column" type="data_column" data_ref="input" />
11 <repeat name="checks" title="Check">
12 <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)">
13 <sanitizer>
14 <valid>
15 <add preset="string.printable"/>
16 <remove value="&#92;" />
17 <remove value="&apos;" />
18 </valid>
19 <mapping initial="none">
20 <add source="&#92;" target="__backslash__" />
21 <add source="&apos;" target="__sq__"/>
22 </mapping>
23 </sanitizer>
24 </param>
25 <param name="replacement" size="40" type="text" value="newchr\1" label="Replacement">
26 <sanitizer>
27 <valid>
28 <add preset="string.printable"/>
29 <remove value="&#92;" />
30 <remove value="&apos;" />
31 </valid>
32 <mapping initial="none">
33 <add source="&#92;" target="__backslash__" />
34 <add source="&apos;" target="__sq__"/>
35 </mapping>
36 </sanitizer>
37 </param>
38 </repeat>
39 </inputs>
40 <outputs>
41 <data format="input" name="out_file1" metadata_source="input" />
42 </outputs>
43 <tests>
44 <test>
45 <param name="input" value="find_tabular_1.txt" ftype="tabular" />
46 <param name="field" value="1" />
47 <param name="pattern" value="moo"/>
48 <param name="replacement" value="cow" />
49 <output name="out_file1" file="replace_tabular_1.txt"/>
50 </test>
51 </tests>
52 <help>
53
54 .. class:: warningmark
55
56 **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.
57
58 .. class:: infomark
59
60 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
61
62 -----
63
64 This tool goes line by line through the specified input file and
65 if the text in the selected column matches a specified regular expression pattern
66 replaces the text with the corresponding specified replacement.
67
68 This tool can be used to change between the chromosome naming conventions of UCSC and Ensembl.
69
70 For example to remove the **chr** part of the reference sequence name in the first column of this GFF file::
71
72 ##gff-version 2
73 ##Date: Thu Mar 23 11:21:17 2006
74 ##bed2gff.pl $Rev: 601 $
75 ##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
76 chr1 bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f 148325916 148325975 . + . score "0";
77 chr21 bed2gff CCDS13614.1_cds_0_0_chr21_32707033_f 32707033 32707192 . + . score "0";
78 chrX bed2gff CCDS14606.1_cds_0_0_chrX_122745048_f 122745048 122745924 . + . score "0";
79
80 Setting::
81
82 using column: c1
83 Find Regex: chr([0-9]+|X|Y|M[Tt]?)
84 Replacement: \1
85
86 produces::
87
88 ##gff-version 2
89 ##Date: Thu Mar 23 11:21:17 2006
90 ##bed2gff.pl $Rev: 601 $
91 ##Input file: ./database/files/61c6c604e0ef50b280e2fd9f1aa7da61.dat
92 1 bed2gff CCDS1000.1_cds_0_0_chr1_148325916_f 148325916 148325975 . + . score "0";
93 21 bed2gff CCDS13614.1_cds_0_0_chr21_32707033_f 32707033 32707192 . + . score "0";
94 X bed2gff CCDS14606.1_cds_0_0_chrX_122745048_f 122745048 122745924 . + . score "0";
95
96
97 This tool uses Python regular expressions with the **re.sub()** function.
98 More information about Python regular expressions can be found here:
99 http://docs.python.org/library/re.html.
100
101 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).
102 Note that the parentheses **()** capture patterns in the text that can be used in the replacement text by using a backslash-number reference: **\\1**
103
104
105
106 Galaxy aggressively escapes input supplied to tools, so if something
107 is not working please let us know and we can look into whether this is
108 the cause. Also if you would like help constructing regular
109 expressions for your inputs, please let us know at help@msi.umn.edu.
110
111 </help>
112 </tool>