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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
author iuc
date Thu, 27 Sep 2018 06:41:00 -0400
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9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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1 <tool id="PlasFlow" name="PlasFlow" version="1.0">
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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2 <description>Prediction of plasmid sequences in metagenomic contigs</description>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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3 <requirements>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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4 <requirement type="package" version="1.1.0">plasflow</requirement>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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5 </requirements>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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6 <command detect_errors="exit_code"><![CDATA[
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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7 PlasFlow.py
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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8 --input '$readFile'
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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9 --output 'output'
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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10 --threshold '$threshold'
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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11 ]]></command>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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12 <inputs>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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13 <param name="readFile" type="data" format="fastq,fasta" optional="true" label="Sequence Reads" />
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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14 <param argument="threshold" type="float" value="0.7" label="Threshold for porbability filtering"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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15 </inputs>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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16 <outputs>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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17 <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" />
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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18 <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" />
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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19 <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" />
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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20 <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" />
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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21 </outputs>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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22 <tests>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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23 <test>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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24 <param name="readFile" value="test.fasta"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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25 <param name="threshold" value="0.7"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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26 <output name="probability_table" value="output"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
iuc
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27 <output name="chromosomes" value="output_chromosomes.fasta"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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28 <output name="plasmids" value="output_plasmids.fasta"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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29 <output name="unclassified" value="output_unclassified.fasta"/>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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30 </test>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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31 </tests>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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32 <help><![CDATA[
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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33 PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. It relies on the neural network models trained on full genome and plasmid sequences and is able to differentiate between plasmids and chromosomes with accuracy reaching 96%. It outperforms other available solutions for plasmids recovery from metagenomes and incorporates the thresholding which allows for exclusion of incertain predictions. PlasFlow has been published in Nucleic Acids Research
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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34 ]]></help>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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35 <citations>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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36 <citation type="doi">10.1093/nar/gkx1321</citation>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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37 </citations>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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38 </tool>
9ae55813ab79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 987797df67fb05506a5d5fa730aa03fd8dd739d8
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39