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comparison virhunter.xml @ 2:ea2cccb9f73e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit c3685ed6a70b47012b62b95a2a3db062bd3b7475
author iuc
date Thu, 05 Jan 2023 14:27:54 +0000
parents 457fd8fd681a
children 302332b914ef
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1:9b12bc1b1e2c 2:ea2cccb9f73e
1 <tool id="virhunter" name="virhunter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="virhunter" name="virhunter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description> 2 <description>
3 Deep learning method to identify viruses in sequencing datasets.. 3 Deep learning method to identify viruses in sequencing datasets
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <xrefs> 8 <xrefs>
22 && cp '${predicted_fragments.extra_files_path}'/predicted.csv predicted.csv 22 && cp '${predicted_fragments.extra_files_path}'/predicted.csv predicted.csv
23 && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta 23 && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta
24 24
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file(s)"/> 27 <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/>
28 <param name="weights" type="select" label="Select a reference model" help="If your model of interest is not listed, contact the Galaxy team"> 28 <param name="weights" type="select" label="Select a reference model" help="If your model of interest is not listed, contact the Galaxy team">
29 <options from_data_table="virhunter_models"> 29 <options from_data_table="virhunter_models">
30 <validator type="no_options" message="No models are available for the selected input dataset" /> 30 <validator type="no_options" message="No models are available for the selected input dataset" />
31 </options> 31 </options>
32 </param> 32 </param>
47 </test> 47 </test>
48 </tests> 48 </tests>
49 49
50 <help> 50 <help>
51 <![CDATA[ 51 <![CDATA[
52 VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequening datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host and bacterial (contamination). 52 VirHunter is a tool that uses deep learning to identify viruses in plant virome sequencing datasets.
53 In particular, VirHunter classifies previously assembled contigs into virus, host and bacteria classes.
53 ]]></help> 54 ]]></help>
54 <expand macro="citations" /> 55 <expand macro="citations" />
55 </tool> 56 </tool>