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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
author iuc
date Mon, 09 Jan 2023 13:27:09 +0000
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b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
iuc
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1 <tool id="decontaminator" name="decontaminator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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2 <description>Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies</description>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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3 <macros>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
iuc
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4 <import>macros.xml</import>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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5 </macros>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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6 <xrefs>
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7 <xref type="bio.tools">decontaminator</xref>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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8 </xrefs>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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9 <expand macro="requirements"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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10 <command detect_errors="exit_code"><![CDATA[
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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11 mkdir -p '${predicted_fragments.extra_files_path}' &&
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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12 python '$__tool_directory__/predict.py'
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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13 --test_ds '${fasta_file}'
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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14 --weights '${weights.fields.path}'
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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15 --out_path '${predicted_fragments.extra_files_path}'
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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16 --return_viral True
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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17 && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.tsv predicted_fragments.tsv
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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18 && cp '${predicted_fragments.extra_files_path}'/predicted.tsv predicted.tsv
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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19 && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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20
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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21 ]]></command>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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22 <inputs>
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23 <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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24 <param name="weights" type="select" label="Select a reference model" help="If your model of interest is not listed, contact the Galaxy team">
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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25 <options from_data_table="decontaminator_models">
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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26 <validator type="no_options" message="No models are available for the selected input dataset" />
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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27 </options>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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28 </param>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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29 </inputs>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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30 <outputs>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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31 <data format="tabular" name="predicted_fragments" from_work_dir="predicted_fragments.tsv" label="${tool.name} on ${on_string}: predicted fragments"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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32 <data format="tabular" name="predicted" from_work_dir="predicted.tsv" label="${tool.name} on ${on_string}: predicted "/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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33 <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" />
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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34 </outputs>
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35 <tests>
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36 <test>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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37 <param name="fasta_file" value="viruses.fasta"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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38 <param name="weights" value="test"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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39 <output name="predicted_fragments" file="predicted_fragments.tsv" ftype="tabular" lines_diff="2"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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40 <output name="predicted" file="predicted.tsv" ftype="tabular" lines_diff="2"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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41 <output name="viral" file="viral.fasta" ftype="fasta" lines_diff="2"/>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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42 </test>
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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43 </tests>
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44 <help>
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45 <![CDATA[
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46 Decontaminator is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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47 sequening datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host and bacterial (contamination).
b856d3d95413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontaminator commit 3f8e87001f3dfe7d005d0765aeaa930225c93b72
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48 ]]></help>
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49 </tool>