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annotate groot.xml @ 0:7af6f7dafd22 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
author iuc
date Fri, 18 Oct 2024 08:19:42 +0000
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0
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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1 <tool id="groot" name="Groot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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2 <description> align reads to references and weight variation graphs and generate report</description>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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3 <macros>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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4 <token name="@TOOL_VERSION@">1.1.2</token>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
iuc
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5 <token name="@VERSION_SUFFIX@">0</token>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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6 <token name="@PROFILE@">22.05</token>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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7 </macros>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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8 <xrefs>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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9 <xref type="bio.tools">groot</xref>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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10 </xrefs>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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11 <requirements>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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12 <requirement type="package" version="@TOOL_VERSION@">groot</requirement>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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13 </requirements>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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14 <command detect_errors="exit_code"><![CDATA[
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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15 set -x pipefail;
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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16 #set $extension = str($fastq.ext)
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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17 ln -s -f '${fastq}' 'input.${extension}' &&
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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18 groot index
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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19 --msaDir '$groot_db_select.fields.path'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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20 --indexDir 'grootIndex'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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21 --windowSize $windowSize
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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22 --kmerSize $kmerSize
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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23 --maxK $maxK
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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24 --maxSketchSpan $maxSketchSpan
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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25 --numPart $numPart
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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26 --sketchSize $sketchSize
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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27 &&
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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28
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29 groot align
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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30 --fastq 'input.${extension}'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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31 --indexDir 'grootIndex'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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32 --contThresh $contThresh
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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33 --minKmerCov $minKmerCov
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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34 --log '$log'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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35 $noAlign
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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36 --processors "\${GALAXY_SLOTS:-1}"
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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37
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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38 | groot report
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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39 --covCutoff '$covCutoff'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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40 $lowCov
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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41 > '$report_out'
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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42
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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43 ]]></command>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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44 <inputs>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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45 <param argument="--fastq" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ file(s) to align"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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46 <section name="index" title="Index">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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47 <param name="groot_db_select" type="select" label="Groot database">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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48 <options from_data_table="groot_database">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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49 <validator message="No groot database is available" type="no_options"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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50 </options>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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51 </param>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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52 <param argument="--windowSize" type="integer" min="0" value="100" label="Size of window to sketch graph traversals" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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53 <param argument="--kmerSize" type="integer" min="0" value="31" label="Size of k-mer" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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54 <param argument="--maxK" type="integer" min="0" value="40" label="maxK in the LSH Ensemble" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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55 <param argument="--maxSketchSpan" type="integer" min="0" value="4" label="Maximum number of identical neighbouring sketches permitted in any graph traversal" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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56 <param argument="--numPart" type="integer" min="0" value="8" label="Number of partitions in the LSH Ensemble" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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57 <param argument="--sketchSize" type="integer" min="0" value="21" label="Size of MinHash sketch" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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58 </section>
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59 <section name="align" title="Align">
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60 <param argument="--contThresh" type="float" min="0" max="1.0" value="0.99" label="Containment threshold for the LSH ensemble" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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61 <param argument="--minKmerCov" type="integer" min="0" value="1" label="Minimum number of k-mers covering each base of a graph segment" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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62 <param argument="--noAlign" type="boolean" truevalue="" falsevalue="--noAlign" label="Perform exact alignment?"
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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63 help="If not, graphs will still be weighted using approximate read mappings"/>
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64 </section>
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65 <section name="report" title="Report">
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66 <param argument="--covCutoff" type="float" min="0" max="1.0" value="0.97" label="Coverage cutoff for reporting ARGs" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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67 <param argument="--lowCov" type="boolean" checked="false" truevalue="--lowCov" falsevalue="" label="Report ARGs which may not be covered at the 5'/3' ends"
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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68 help="If 'Yes', overrides --covCutoff option"/>
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69 </section>
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70 </inputs>
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71 <outputs>
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72 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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73 <data name="report_out" format="tabular" label="${tool.name} on ${on_string}: Report"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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74 </outputs>
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75 <tests>
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76 <test expect_num_outputs="2">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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77 <param name="fastq" value="bla-b7-150bp-5x.fq" ftype="fastq"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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78 <section name="index">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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79 <param name="groot_db_select" value="resfinder.90" />
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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80 <param name="windowSize" value="150"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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81 <param name="kmerSize" value="31"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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82 <param name="maxK" value="20"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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83 <param name="maxSketchSpan" value="30"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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84 <param name="numPart" value="8"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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85 <param name="sketchSize" value="20"/>
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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86 </section>
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87 <section name="align">
7af6f7dafd22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/groot commit 85ca2a9a7b2871674dbb9e53e398e459debca529
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88 <param name="contThresh" value="0.99"/>
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89 <param name="minKmerCov" value="1" />
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90 <param name="noAlign" value=""/>
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91 </section>
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92 <section name="report">
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93 <conditional name="arg_report">
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94 <param name="criteria" value="cutoff" />
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95 <param name="covCutoff" value="0.97" />
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96 </conditional>
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97 </section>
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98 <output name="report_out" ftype="tabular">
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99 <assert_contents>
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100 <has_text text="blaB-7_1_AF189304"/>
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101 <has_n_lines n="1"/>
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102 <has_n_columns n="4"/>
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103 </assert_contents>
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104 </output>
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105 <output name="log" ftype="txt">
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106 <assert_contents>
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107 <has_text text="version"/>
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108 <has_text text="1.1.2"/>
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109 </assert_contents>
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110 </output>
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111 </test>
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112 <test expect_num_outputs="2">
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113 <param name="fastq" value="argannot_light-150bp-10000-reads.fq.gz" ftype="fastq.gz"/>
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114 <section name="index">
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115 <param name="groot_db_select" value="arg-annot.90" />
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116 <param name="windowSize" value="150"/>
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117 <param name="kmerSize" value="41"/>
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118 <param name="maxK" value="4"/>
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119 <param name="maxSketchSpan" value="30"/>
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120 <param name="numPart" value="8"/>
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121 <param name="sketchSize" value="21"/>
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122 </section>
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123 <section name="align">
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124 <param name="contThresh" value="0.99"/>
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125 <param name="minKmerCov" value="1" />
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126 <param name="noAlign" value=""/>
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127 </section>
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128 <section name="report">
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129 <param name="covCutoff" value="0.97" />
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130 <param name="lowCov" value="True"/>
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131 </section>
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132 <output name="report_out" ftype="tabular">
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133 <assert_contents>
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134 <has_text text="argannot~~~(Bla)VIM-9~~~AY524988:1-801"/>
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135 <has_text text="argannot~~~(Bla)VIM-20~~~GQ414736:1-801"/>
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136 <has_n_lines n="5"/>
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137 <has_n_columns n="4"/>
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138 </assert_contents>
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139 </output>
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140 <output name="log" ftype="txt">
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141 <assert_contents>
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142 <has_text text="version"/>
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143 <has_text text="1.1.2"/>
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144 </assert_contents>
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145 </output>
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146 </test>
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147 </tests>
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148 <help><![CDATA[
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149 **What it does**
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150
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151 GROOT is a tool to profile Antibiotic Resistance Genes (ARGs) in metagenomic samples.
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152
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153 The method combines variation graph representation of gene sets with an LSH Forest
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154 indexing scheme to allow for fast classification of metagenomic reads using
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155 similarity-search queries. Subsequent hierarchical local alignment of classified reads
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156 against graph traversals facilitates accurate reconstruction of full-length gene sequences
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157 using a scoring scheme.
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158
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159 The main advantages of GROOT over existing tools are:
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160
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161 - quick classification of reads to candidate ARGs
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162 - accurate annotation of full-length ARGs
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163 - can run on a laptop in minutes
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164
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165 GROOT aligns reads to ARG variation graphs, producing an alignment file that contains
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166 the graph traversals possible for each query read. The alignment file is then used to
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167 generate a simple resistome profile report.
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168
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169 **Output**
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170
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171 GROOT will output an ARG alignment file (in BAM format) that contains the graph traversals possible for each query read; the alignment file is then used by GROOT to generate a resistome profile.
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172
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173 ]]></help>
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174 <citations>
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175 <citation type="doi">10.1093/bioinformatics/bty387</citation>
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176 </citations>
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177 </tool>