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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
author dfornika
date Tue, 28 Jan 2020 01:18:59 +0000
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419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
dfornika
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1 <?xml version="1.0"?>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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2 <tool id="mashtree" name="mashtree" version="@VERSION@+galaxy0">
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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3 <description>Create a tree using Mash distances.</description>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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4 <requirements>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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5 <requirement type="package" version="@VERSION@">mashtree</requirement>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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6 </requirements>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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7 <command><![CDATA[
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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8 mashtree
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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9 --numcpus "\${GALAXY_SLOTS:-1}"
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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10 --genomesize '${genomesize}'
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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11 --mindepth '${mindepth}'
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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12 --outmatrix '${matrix}'
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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13 --outtree '${tree}'
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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14
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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15 ]]></command>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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16
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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17 <inputs>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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18 <conditional name="fastq_input">
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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19 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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20 <option value="paired">Paired</option>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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21 <option value="single">Single</option>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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22 <option value="paired_collection">Paired Collection</option>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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23 <option value="paired_iv">Paired Interleaved</option>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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24 </param>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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25 <when value="paired">
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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26 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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27 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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28 </when>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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29 <when value="single">
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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30 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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31 </when>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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32 <when value="paired_collection">
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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33 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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34 </when>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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35 </conditional>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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36 <param name="genomesize" type="integer" min="1000" value="5000000" max="50000000" />
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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37 <param name="mindepth" type="integer" min="0" value="5" max="100" />
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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38 <param name="kmerlength" type="integer" min="4" value="21" max="31" />
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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39 <param name="sketch-size" type="integer" min="100" value="10000" max="100000" />
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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40 </inputs>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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41
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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42 <outputs>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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43 <data name="tree" format="" label="${tool.name} on ${on_string}: Tree" />
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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44 <data name="matrix" format="tabular" label="${tool.name} on ${on_string}: Distance matrix" />
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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45 </outputs>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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46
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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47 <tests>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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48
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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49 </tests>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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50 <help><![CDATA[
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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51
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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52 ]]></help>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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53 <citations>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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54 </citations>
419ea5baf5b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashtree commit 9b894593cf3c0156faf679300ded731e0796f792"
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55 </tool>