Mercurial > repos > genouest > logol

annotate logol.xml @ 0:f11370aba286 draft

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
author genouest
date Wed, 06 Jun 2018 10:35:32 -0400
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children 08a6fd2620b3
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f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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1 <?xml version="1.0"?>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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2 <tool id="logol_wrapper" name="Logol" version="1.7.8">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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3 <description>Biological patterns matching</description>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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4 <requirements>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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5 <requirement type="package" version="1.7.8=1">logol</requirement>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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6 <requirement type="package" version="6.0">unzip</requirement>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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7 </requirements>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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8 <command detect_errors="exit_code"><![CDATA[
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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9
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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10 ## generate properties file
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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11 echo -e "minSplitSize=2000000\nmaxResultSize=0\nmaxMatchSize=0\nworkingDir=.\ndir.result=.\nmaxSpacerLength=0\nmaxLength=0\nminLength=2\nparentStrategy=1\nnbProcessor=1\nnbJobs=1\nmaxSolutions=100\nminTreeIndex=2\nsuffix.tool = 2" > logol.properties
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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12
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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13 &&
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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15 LogolMultiExec.sh
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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16 #if str( $options_input.options_input_selector ) == "model":
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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17 -m ${options_input.m}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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18 #else
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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19 -g ${options_input.g}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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20 #end if
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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21
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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22 -${type}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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23 -s ${s}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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24 -max ${max}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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26 ${fasta}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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27 ${gff}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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28 ${all}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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29
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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30 -maxmatchsize ${maxmatchsize}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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31 -maxspacer ${maxspacer}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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32 -lmax ${lmax}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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33 -lmin ${lmin}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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34
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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35 ${forcesplit}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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36
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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37 -conf logol.properties
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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38
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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39 -out 'logol_results.zip'
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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40
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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41 > ${log_file}
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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42
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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43 &&
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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44
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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45 unzip logol_results.zip
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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46
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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47 ]]></command>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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48
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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49 <inputs>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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50 <conditional name="options_input">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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51 <param name="options_input_selector" type="select" label="Logol pattern type">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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52 <option value="model" selected="True">Logol pattern model</option>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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53 <option value="grammar">Logol pattern grammar</option>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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54 </param>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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55 <when value="model">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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56 <param argument="-m" type="data" format="txt" label="Logol pattern model" help="Pattern model designed by LogolDesigner" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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57 </when>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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58 <when value="grammar">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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59 <param argument="-g" type="data" format="txt" label="Logol pattern grammar" help="Logol Grammar file" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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60 </when>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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61 </conditional>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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62
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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63 <param name="type" type="select" format="text">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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64 <label>Type of personal data file</label>
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65 <option value="dna">DNA</option>
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66 <option value="rna">RNA</option>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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67 <option value="protein">PROTEIN</option>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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68 </param>
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69
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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70 <param argument="-s" type="data" format="fasta" label="Read from file" help="Fasta sequence to analyse" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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71
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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72 <param argument="-max" type="integer" value="100" label="Maximum number of result matches"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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73 <param argument="-fasta" type="boolean" truevalue="-fasta" falsevalue="" label="Add fasta conversion to result archive" checked="False" value="False"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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74 <param argument="-gff" type="boolean" truevalue="-gff" falsevalue="" label="Add gff conversion to result archive" checked="False" value="False"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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75 <param argument="-all" type="boolean" truevalue="-all" falsevalue="" label="Search sequence in both directions" checked="False" value="False"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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76 <param argument="-maxmatchsize" type="integer" value="0" label="Maximum size of a match (0 is no limit)"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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77 <param argument="-maxspacer" type="integer" value="0" label="Maximum size of a spacer (0 is no limit)"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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78 <param argument="-lmax" type="integer" value="0" label="Maximum size of a word (0 is no limit)"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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79 <param argument="-lmin" type="integer" value="2" label="Minimum size of a word"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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80 <param argument="-forcesplit" truevalue="-forcesplit" falsevalue="" type="boolean" label="Allow sequence cut (if several models are defined in rule, all models will look for pattern in same sequence range" checked="False" value="False"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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81 <param name="zip" type="boolean" label="Generate zip archive with all files" checked="False" value="False" help="Zip file contains all xml and fasta/gff files if conversion is activated"/>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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82
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83 </inputs>
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84 <outputs>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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85 <data format="txt" name="log_file" label="Log : ${tool.name} on ${on_string}" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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86 <data format="zip" name="logol_results_archive" from_work_dir="logol_results.zip" label="Compressed files : ${tool.name} on ${on_string}">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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87 <filter>zip</filter>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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88 </data>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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89 <collection name="logol_results" type="list" label="XML files: ${tool.name} on ${on_string}">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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90 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml$" ext="xml" visible="false" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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91 </collection>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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92 <collection name="logol_results_gff" type="list" label="GFF files: ${tool.name} on ${on_string}">
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93 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml\.gff" ext="gff" visible="false" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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94 <filter>gff</filter>
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95 </collection>
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96 <collection name="logol_results_fasta" type="list" label="Fasta files: ${tool.name} on ${on_string}">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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97 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml\.fasta" ext="fasta" visible="false" />
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98 <filter>fasta</filter>
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99 </collection>
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100 </outputs>
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101 <tests>
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102 <test>
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103 <param name="s" value="primer.fasta" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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104 <conditional name="options_input">
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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105 <param name="options_input_selector" value="grammar"/>
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106 <param name="g" value="primer.logol" />
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107 </conditional>
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108 <param name="zip" value="True" />
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109 <output name="logol_results_archive" compare="sim_size" file="logol_results.zip" />
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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110 </test>
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111 <test>
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112 <param name="s" value="primer.fasta" />
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113 <conditional name="options_input">
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114 <param name="options_input_selector" value="grammar"/>
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115 <param name="g" value="primer.logol" />
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116 </conditional>
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117 <param name="gff" value="True" />
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118 <param name="fasta" value="True" />
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119 <param name="forcesplit" value="True" />
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120 <param name="all" value="True" />
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121 <param name="zip" value="True" />
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122 <output name="logol_results_archive" compare="sim_size" file="logol_results_multi_format.zip" />
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123 </test>
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124 </tests>
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125
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126 <help><![CDATA[
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127
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128 Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).
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129
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130 It includes a Linux command line tool and a graphical designer.
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131
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132 http://logol.genouest.org/web/app.php/logol
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133
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134 -------------------------------------------------------------------------
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135
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136 Software is free and open source, under CeCILL license
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137
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138
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139 ]]></help>
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140 <citations>
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141 <citation type="doi">10.1007/978-3-319-09192-1_4</citation>
f11370aba286 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
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142 </citations>
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143 </tool>