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