Mercurial > repos > geert-vandeweyer > advanced_grep_from_file
comparison GrepFile.xml @ 0:fd6b71c81011 draft
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| author | geert-vandeweyer |
|---|---|
| date | Thu, 13 Feb 2014 08:37:16 -0500 |
| parents | |
| children | 94ba1a8de091 |
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| -1:000000000000 | 0:fd6b71c81011 |
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| 1 <tool id="GrepFile" name="Grep File" version="0.0.1"> | |
| 2 <description></description> | |
| 3 <command interpreter="perl">GrepFile.pl | |
| 4 -i "$input" | |
| 5 -o "$output" | |
| 6 | |
| 7 ## perl/case triggers | |
| 8 $perl | |
| 9 | |
| 10 ## return extra lines after the match (eg fasta/fastq grepping) | |
| 11 #if $extralines.extra == "true": | |
| 12 -A $extralines.nr | |
| 13 #end if | |
| 14 | |
| 15 ## grep from file or grep from provided pattern | |
| 16 #if $PatSource.fromfile == "true": | |
| 17 -t "file" | |
| 18 -f "$PatSource.patternfile" | |
| 19 #else: | |
| 20 -t "single" | |
| 21 -f "$PatSource.pattern" | |
| 22 #end if | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="input" type="data" label="Input file" help="text/tabular/fasta/sam/... file to extract the matches from"/> | |
| 26 <conditional name="extralines"> | |
| 27 <param name="extra" type="select" label="Fetch Extra Lines" help="Also fetch lines following the matched pattern (eg for fastq extraction based on readname)"> | |
| 28 <option value="true" >Yes</option> | |
| 29 <option value="false" selected="True">No</option> | |
| 30 </param> | |
| 31 <when value="true"> | |
| 32 <param name="nr" type="integer" value="1" label="Extra lines to fetch" /> | |
| 33 </when> | |
| 34 </conditional> | |
| 35 <conditional name="PatSource"> | |
| 36 <param name="fromfile" type="select" label="Pattern Source" > | |
| 37 <option value="true" >Pattern File</option> | |
| 38 <option value="false" >Single Pattern</option> | |
| 39 </param> | |
| 40 <when value="true"> <param name="patternfile" type="data" label="Pattern File" help="A text file with one pattern per line" /> | |
| 41 </when> | |
| 42 <when value="false"> | |
| 43 <param name="pattern" type="text" label="Pattern" help="Provide a valid grep pattern" /> | |
| 44 | |
| 45 </when> | |
| 46 </conditional> | |
| 47 <param name="perl" type="select" label="Matching type"> | |
| 48 <option value="">Exact string matching</option> | |
| 49 <option value="-i">Case Insensitive matching (slower!)</option> | |
| 50 <option value="-P">Interpret patterns as Perl Regex</option> | |
| 51 </param> | |
| 52 | |
| 53 </inputs> | |
| 54 <outputs> | |
| 55 <data format="input" name="output" metadata_source="input"/> | |
| 56 </outputs> | |
| 57 <help> | |
| 58 | |
| 59 **What it does** | |
| 60 | |
| 61 This tool extends the grepping options available in galaxy. It allowes extracting lines following a match, grepping from a file of patterns, and perl-based matching. | |
| 62 | |
| 63 </help> | |
| 64 </tool> |