Mercurial > repos > geert-vandeweyer > advanced_grep_from_file
view GrepFile.xml @ 1:dba6ffec8e2e draft
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author | geert-vandeweyer |
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date | Thu, 13 Feb 2014 08:37:30 -0500 |
parents | fd6b71c81011 |
children | 94ba1a8de091 |
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<tool id="GrepFile" name="Grep File" version="0.0.1"> <description></description> <command interpreter="perl">GrepFile.pl -i "$input" -o "$output" ## perl/case triggers $perl ## return extra lines after the match (eg fasta/fastq grepping) #if $extralines.extra == "true": -A $extralines.nr #end if ## grep from file or grep from provided pattern #if $PatSource.fromfile == "true": -t "file" -f "$PatSource.patternfile" #else: -t "single" -f "$PatSource.pattern" #end if </command> <inputs> <param name="input" type="data" label="Input file" help="text/tabular/fasta/sam/... file to extract the matches from"/> <conditional name="extralines"> <param name="extra" type="select" label="Fetch Extra Lines" help="Also fetch lines following the matched pattern (eg for fastq extraction based on readname)"> <option value="true" >Yes</option> <option value="false" selected="True">No</option> </param> <when value="true"> <param name="nr" type="integer" value="1" label="Extra lines to fetch" /> </when> </conditional> <conditional name="PatSource"> <param name="fromfile" type="select" label="Pattern Source" > <option value="true" >Pattern File</option> <option value="false" >Single Pattern</option> </param> <when value="true"> <param name="patternfile" type="data" label="Pattern File" help="A text file with one pattern per line" /> </when> <when value="false"> <param name="pattern" type="text" label="Pattern" help="Provide a valid grep pattern" /> </when> </conditional> <param name="perl" type="select" label="Matching type"> <option value="">Exact string matching</option> <option value="-i">Case Insensitive matching (slower!)</option> <option value="-P">Interpret patterns as Perl Regex</option> </param> </inputs> <outputs> <data format="input" name="output" metadata_source="input"/> </outputs> <help> **What it does** 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. </help> </tool>