Mercurial > repos > iuc > obi_annotate

annotate obiclean.xml.orig @ 4:d0f6ac976373 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:49:38 +0000
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4
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <<<<<<< HEAD
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <description>tags a set of sequences for PCR/sequencing errors identification</description>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <import>macros.xml</import>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 <expand macro="requirements"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 <expand macro="stdio"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 <command><![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 @GUNZIP_INPUT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 obiclean
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 --without-progress-bar
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 #if $distance
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 -d '$distance'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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17 #if $key
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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18 -s '$key'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20 #if $ratio
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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21 -r '$ratio'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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23 ${head}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24 @INPUT_FORMAT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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25 @OUT_FORMAT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26 input
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27 @GZIP_OUTPUT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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28 >'$output'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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29 @GENERATE_GALAXY_JSON@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 ]]></command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 <inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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32 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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36 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 <expand macro="input_format_options_macro"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 <expand macro="out_format_macro"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 </inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 <outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 <data format="auto" name="output"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 </outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43 <tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 <param name="input" value="output_obiannotate.fasta" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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46 <param name="head" value="True"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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47 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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49 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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50 <param name="input" value="output_obiannotate.fasta.gz" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 <param name="key" value="merged_sample"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52 <param name="ratio" value="0.05"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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53 <param name="head" value="False"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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54 <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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56 </tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 <help><![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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58
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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59 .. class:: infomark
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60
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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61 **What it does**
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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63 obijoinpairedend aims at joining the two reads of a paired-end library.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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64
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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66
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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67 The program uses as input one or two sequences reads files.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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68
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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69 If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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70 If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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71
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72 @OBITOOLS_LINK@
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73
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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74 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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75 </help>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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76 <expand macro="citation" />
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77 </tool>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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78 =======
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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79 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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80 <description>tags a set of sequences for PCR/sequencing errors identification</description>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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81 <expand macro="bio_tools"/>
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82 <macros>
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83 <import>macros.xml</import>
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84 </macros>
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85 <expand macro="requirements"/>
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86 <expand macro="stdio"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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87
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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88 <command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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89
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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90 <![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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91 obiclean
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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92
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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93 #if $distance
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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94 -d '$distance'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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95 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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96 #if $key
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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97 -s '$key'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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98 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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99 #if $ratio
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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100 -r '$ratio'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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101 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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102 ${head}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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103
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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104 '$input'>'$output'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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105
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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106
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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107 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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108
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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109 </command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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110
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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111 <inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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112 <param name="input" type="data" format="fasta" label="Input sequences file" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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113 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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114 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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115 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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116 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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117 </inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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118 <outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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119 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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120 </outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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121 <tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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122 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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123 <param name="input" value="output_obiannotate.fasta" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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124 <param name="head" value="True"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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125 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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126 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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127 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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128 <param name="input" value="output_obiannotate.fasta" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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129 <param name="key" value="merged_sample"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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130 <param name="ratio" value="0.05"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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131 <param name="head" value="False"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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132 <output name="output" file="output_obiclean_advanced.fasta" ftype="fasta"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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133 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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134 </tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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135 <help><![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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136
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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137 .. class:: infomark
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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138
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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139 **What it does**
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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140
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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141 obijoinpairedend aims at joining the two reads of a paired-end library.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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142
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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143 For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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144
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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145 The program uses as input one or two sequences reads files.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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146
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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147 If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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148 If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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149
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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150 @OBITOOLS_LINK@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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151
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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152 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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153 </help>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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154 <expand macro="citation" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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155 </tool>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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156 >>>>>>> 7abad681f (add tools up until P)