annotate GrepFile.xml @ 7:418e58465a5a draft default tip

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1 <tool id="GrepFile" name="Advanced Grep" version="0.0.1">
2   <description></description>
3   <requirements>
4 		<requirement type='package' version='1.92'>perl_module_threads</requirement>
5 		<requirement type='package' version='1.46'>perl_module_threads_shared</requirement>
6 		<requirement type='package' version='3.02'>perl_module_Thread_Queue</requirement>
7 
8         </requirements>
9 
10   <command  interpreter="perl">GrepFile.pl
11 	-i "$input"
12 	-o "$output"
13 	
14 	## perl/case triggers
15 	$perl
16 	 
17 	## return extra lines after the match (eg fasta/fastq grepping)
18 	#if $extralines.extra == "true":
19 		-A $extralines.nr
20 	#end if
21 
22 	## grep from file or grep from provided pattern
23 	#if $PatSource.fromfile == "true":
24 		-t "file"
25 		-f "$PatSource.patternfile"
26 	#else:
27 		-t "single"
28 		-f "$PatSource.pattern"
29 	#end if
30   </command>
31   <inputs>
32     <param name="input" type="data" label="Input file" help="text/tabular/fasta/sam/... file to extract the matches from"/>
33     <conditional name="extralines">
34       <param name="extra" type="select" label="Fetch Extra Lines" help="Also fetch lines following the matched pattern (eg for fastq extraction based on readname)">
35         <option value="true" >Yes</option>
36         <option value="false" selected="True">No</option>
37       </param>
38       <when value="true">
39 	<param name="nr" type="integer" value="1" label="Extra lines to fetch" />
40       </when>
41     </conditional>
42    <conditional name="PatSource">
43       <param name="fromfile" type="select" label="Pattern Source" >
44         <option value="true" >Pattern File</option>
45         <option value="false" >Single Pattern</option>
46       </param>
47       <when value="true"> 	<param name="patternfile" type="data" label="Pattern File" help="A text file with one pattern per line" />
48      </when>
49       <when value="false">
50 	<param name="pattern" type="text" label="Pattern" help="Provide a valid grep pattern" ><sanitizer sanitize="False" /></param>
51 	
52       </when>
53     </conditional>
54     <param name="perl" type="select" label="Matching type">
55 	<option value="">Exact string matching</option>
56 	<option value="-i">Case Insensitive matching (slower!)</option>
57 	<option value="-P">Interpret patterns as Perl Regex</option>
58     </param>
59 
60   </inputs>
61   <outputs>
62     <data format="input" name="output" metadata_source="input"/>
63   </outputs>
64     <help>
65 
66 **What it does**
67 
68 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.
69 
70     </help>
71 </tool>