vibrant: vibrant.xml annotate

annotate vibrant.xml @ 1:353fc14d89aa draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b

author	ufz
date	Mon, 12 May 2025 13:57:42 +0000
parents	b238f5afa054
children

rev	line source
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	1 <tool id="vibrant" name="VIBRANT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	2 <description></description>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	3 <macros>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	4 <token name="@TOOL_VERSION@">1.2.1</token>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	5 <token name="@VERSION_SUFFIX@">2</token>
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	6 </macros>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	7 <xrefs>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	8 <xref type="bio.tools">VIBRANT</xref>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	9 </xrefs>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	10 <requirements>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">vibrant</requirement>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	12 </requirements>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	14 ## link input in order to have a predictable output name
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	15 ln -s '$input' 'input.fas' &&
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	16
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	17 VIBRANT_run.py
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	18 -i 'input.fas'
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	19 $protein
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	20 -d '${database.fields.path}/databases/'
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	21 -m '${database.fields.path}/files/'
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	22 -l $l
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	23 -o $o
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	24 $virome
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	25 -t "\${GALAXY_SLOTS:-1}"
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	26 ]]></command>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	27 <inputs>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	28 <param argument="-i" name="input" type="data" format="fasta" label="Input FASTA file"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	29 <param argument="-f" name="protein" type="boolean" truevalue="-f prot" falsevalue="-f nucl" checked="false" label="Input is protein" help="By default nucleotide sequence is assumed"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	30 <param argument="-d" name="database" type="select" label="Reference data">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	31 <options from_data_table="vibrant"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	32 </param>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	33 <param argument="-l" type="integer" value="1000" min="1000" label="Minumum scaffold length" help="VIBRANT will only consider scaffolds greater than or equal to this value"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	34 <param argument="-o" type="integer" value="4" min="4" label="Minumum number of ORFs" help="VIBRANT will only consider scaffolds with at least this number of ORFs"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	35 <param argument="-virome" type="boolean" truevalue="--virome" falsevalue="" checked="false" label="Input is virome" help="This flag should be used cautiously. This will edit VIBRANT's sensitivity if the input dataset is a virome and not mixed metagenome. That is, if you expect the vast majority of your input scaffolds to be viruses then -virome can be used to remove obvious non-viral scaffolds. This will have no effect on runtime."/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	36 <param name="outputs" type="select" multiple="true" optional="false" label="Outputs" help="Outputs marked with \* are not available for protein input. ">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	37 <option value="log_run">Run log file</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	38 <option value="figures" selected="true">Figures</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	39 <option value="phages_circular_fna">Circular virus genomes *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	40 <option value="phages_combined_faa">Virus encoded proteins</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	41 <option value="phages_combined_ffn">Virus encoded genes *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	42 <option value="phages_combined_fna" selected="true">All virus genomes (fasta) *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	43 <option value="phages_combined_gbk" selected="true">All virus genomes (genbank) *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	44 <option value="phages_combined_txt" selected="true">All virus genome names</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	45 <option value="phages_lysogenic_faa">Lysogenic virus encoded proteins</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	46 <option value="phages_lysogenic_ffn">Lysogenic virus encoded genes *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	47 <option value="phages_lysogenic_fna">Lysogenic virus genomes (fasta) *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	48 <option value="phages_lytic_faa">Lytic virus encoded proteins</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	49 <option value="phages_lytic_ffn">Lytic virus encoded genes *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	50 <option value="phages_lytic_fna">Lytic virus genomes (fasta) *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	51 <option value="AMG_counts">All predicted virus AMGs</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	52 <option value="AMG_individuals">Individual predicted virus AMGs by protein and its respective genome</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	53 <option value="AMG_pathways">Summary of the present KEGG metabolic pathways corresponding to virus AMGs</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	54 <option value="annotations">Annotations and associated information for KEGG, Pfam and VOG</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	55 <option value="complete_circular">Virus genomes that were predicted to be circular and therefore complete genomes *</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	56 <option value="figure_PCA">Scaffold coordinatesfor each viral scaffold on the PCA plot</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	57 <option value="genbank_table">Single annotation used for all predicted virus proteins</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	58 <option value="genome_quality">Predicted genome quality and type</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	59 <option value="integrated_prophage_coordinates">Scaffold/genome coordinate information of each integrated provirus that was excised from a host scaffold</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	60 <option value="machine">Summary of predictions made by the neural network machine learning classifier.</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	61 <option value="summary_normalized">Complete annotation normalized summary metrics for each predicted virus genome</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	62 <option value="summary_results">Complete annotation summary metrics for each predicted virus genome</option>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	63 </param>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	64 </inputs>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	65 <outputs>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	66 <data name="log_run" format="txt" from_work_dir="VIBRANT_log_run_input.log" label="${tool.name} on ${on_string}: Run log file">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	67 <filter>"log_run" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	68 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	69 <collection name="figures" type="list" format="pdf" label="${tool.name} on ${on_string}: Figures">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	70 <discover_datasets directory="VIBRANT_input/VIBRANT_figures_input" pattern="VIBRANT_figure_(?P<designation>.*)_input\.pdf"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	71 <filter>"figures" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	72 </collection>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	73 <!-- files form VIBRANT_phages_input FASTA and associated files for predicted viruses. -->
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	74 <data name="phages_circular_fna" format="fasta" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_circular.fna" label="${tool.name} on ${on_string}: Circular virus genomes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	75 <filter>"phages_circular_fna" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	76 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	77 <data name="phages_combined_faa" format="fasta" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_combined.faa" label="${tool.name} on ${on_string}: Virus encoded proteins">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	78 <filter>"phages_combined_faa" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	79 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	80 <data name="phages_combined_ffn" format="fasta" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_combined.ffn" label="${tool.name} on ${on_string}: Virus encoded genes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	81 <filter>"phages_combined_ffn" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	82 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	83 <data name="phages_combined_fna" format="fasta" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_combined.fna" label="${tool.name} on ${on_string}: Virus genomes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	84 <filter>"phages_combined_fna" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	85 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	86 <data name="phages_combined_gbk" format="genbank" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_combined.gbk" label="${tool.name} on ${on_string}: Virus genomes genbank">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	87 <filter>"phages_combined_gbk" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	88 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	89 <data name="phages_combined_txt" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_combined.txt" label="${tool.name} on ${on_string}: Virus genome names">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	90 <filter>"phages_combined_txt" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	91 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	92 <data name="phages_lysogenic_faa" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lysogenic.faa" label="${tool.name} on ${on_string}: Lysogenic virus encoded proteins">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	93 <filter>"phages_lysogenic_faa" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	94 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	95 <data name="phages_lysogenic_ffn" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lysogenic.ffn" label="${tool.name} on ${on_string}: Lysogenic virus encoded genes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	96 <filter>"phages_lysogenic_ffn" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	97 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	98 <data name="phages_lysogenic_fna" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lysogenic.fna" label="${tool.name} on ${on_string}: Lysogenic virus genomes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	99 <filter>"phages_lysogenic_fna" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	100 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	101 <data name="phages_lytic_faa" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lytic.faa" label="${tool.name} on ${on_string}: Lytic virus encoded proteins">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	102 <filter>"phages_lytic_faa" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	103 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	104 <data name="phages_lytic_ffn" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lytic.ffn" label="${tool.name} on ${on_string}: Lytic virus encoded genes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	105 <filter>"phages_lytic_ffn" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	106 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	107 <data name="phages_lytic_fna" format="txt" from_work_dir="VIBRANT_input/VIBRANT_phages_input/input.phages_lytic.fna" label="${tool.name} on ${on_string}: Lytic virus genomes">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	108 <filter>"phages_lytic_fna" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	109 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	110 <data name="AMG_counts" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_counts_input.tsv" label="${tool.name} on ${on_string}: Predicted virus AMGs">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	111 <filter>"AMG_counts" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	112 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	113 <data name="AMG_individuals" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_individuals_input.tsv" label="${tool.name} on ${on_string}: Individual predicted virus AMGs">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	114 <filter>"AMG_individuals" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	115 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	116 <data name="AMG_pathways" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_AMG_pathways_input.tsv" label="${tool.name} on ${on_string}: KEGG metabolic pathways corresponding to virus AMGs">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	117 <filter>"AMG_pathways" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	118 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	119 <data name="annotations" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_annotations_input.tsv" label="${tool.name} on ${on_string}: Annotations for KEGG, Pfam and VOG">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	120 <filter>"annotations" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	121 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	122 <data name="complete_circular" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_complete_circular_input.tsv" label="${tool.name} on ${on_string}: Complete circular genomes ">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	123 <filter>"complete_circular" in outputs and not protein</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	124 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	125 <data name="figure_PCA" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_figure_PCA_input.tsv" label="${tool.name} on ${on_string}: Scaffold coordinates on the PCA plot">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	126 <filter>"figure_PCA" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	127 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	128 <data name="genbank_table" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_genbank_table_input.tsv" label="${tool.name} on ${on_string}: Single annotation used for all predicted virus proteins">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	129 <filter>"genbank_table" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	130 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	131 <data name="genome_quality" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_genome_quality_input.tsv" label="${tool.name} on ${on_string}: Predicted genome quality and type">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	132 <filter>"genome_quality" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	133 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	134 <data name="integrated_prophage_coordinates" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_integrated_prophage_coordinates_input.tsv" label="${tool.name} on ${on_string}: Coordinates of integrated provirus">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	135 <filter>"integrated_prophage_coordinates" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	136 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	137 <data name="machine" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_machine_input.tsv" label="${tool.name} on ${on_string}: Predictions of the neural network classifier">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	138 <filter>"machine" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	139 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	140 <data name="summary_normalized" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_summary_normalized_input.tsv" label="${tool.name} on ${on_string}: Normalized summary metrics">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	141 <filter>"summary_normalized" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	142 </data>
1 353fc14d89aa planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit 9cdc0038a53dff0749a3da0a28b7f373617f994b ufz parents: 0 diff changeset	143 <data name="summary_results" format="tabular" from_work_dir="VIBRANT_input/VIBRANT_results_input/VIBRANT_summary_results_input.tsv" label="${tool.name} on ${on_string}: Summary metrics">
0 b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	144 <filter>"summary_results" in outputs</filter>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	145 </data>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	146 <!-- files from VIBRANT_results_input. Folder containing useful tab-delimited files -->
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	147 <!--
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	148 ├── input.prodigal.faa Prodigal predicted proteins for all input scaffolds.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	149 ├── input.prodigal.ffn genes for all input scaffolds
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	150 ├── input.prodigal.gff gff file for all input scaffolds
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	151 ├── VIBRANT_figures_input Folder containing PDF figures summarizing outputs
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	152 │ ├── VIBRANT_figure_pathways_input.pdf Graphical summary (bar plot) of KEGG pathways for identified viral AMG
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	153 │ ├── VIBRANT_figure_PCA_input.pdf PCA plot summarizing predicted viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	154 │ ├── VIBRANT_figure_phages_input.pdf Graphical summary (nested bubble plot) for ratio of total input scaffolds (outside), number of scaffolds that were greater than or equal to minimum size restrictions (middle), and number of identified viruses (inside). Must have at least 10 input sequences for this file to be present. The represented numbers can be found in the run log file (#20)
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	155 │ ├── VIBRANT_figure_quality_input.pdf Graphical summary (bar plot) of number of viruses per genome quality category
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	156 │ └── VIBRANT_figure_sizes_input.pdf Graphical summary (histogram) of genome sizes of identified viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	157 ├── VIBRANT_HMM_tables_parsed_input Folder containing parsed HMM table raw outputs. Any one of the contained files may be empty. This folder is likely not of use but contains non-redundant annotation information. Contains both virus and non-virus annotation
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	158 │ ├── input.KEGG_hmmtbl_parse.tsv KEGG parsed HMM table raw outputs.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	159 │ ├── input.Pfam_hmmtbl_parse.tsv Pfam parsed HMM table raw outputs
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	160 │ └── input.VOG_hmmtbl_parse.tsv VOG parsed HMM table raw outputs
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	161 ├── VIBRANT_HMM_tables_unformatted_input Folder containing non-parsed (unformatted) HMM complete raw outputs. Any one of the contained files may be empty. This folder is likely not of use but contains complete annotation information. Contains both virus and non-virus annotations:
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	162 │ ├── input_unformatted_KEGG.hmmtbl
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	163 │ ├── input_unformatted_Pfam.hmmtbl
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	164 │ └── input_unformatted_VOG.hmmtbl
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	165 ├── VIBRANT_log_annotation_input.log Annotation log file. This log will be empty unless an error was encountered during the annotation component of VIBRANT
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	166 ├── VIBRANT_log_run_input.log Run log file. Contains information about the command used, the total runtime, date of run, version of VIBRANT, and summary of values used in file #8. This log file is more of a run and output summary file, though in the event of an error the message will be displayed in this log file
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	167 ├── VIBRANT_phages_input Folder containing FASTA and associated files for predicted viruses. Any one of the contained files may be empty if no viruses fit the criteria. Lysogenic viruses are determined by any virus scaffold excised from a larger scaffold or any that encodes an integrase. Lytic viruses are all others. For identified viruse
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	168 │ ├── input.phages_circular.fna All virus genomes identified as circular.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	169 │ ├── input.phages_combined.faa All virus encoded proteins.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	170 │ ├── input.phages_combined.ffn All virus encoded genes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	171 │ ├── input.phages_combined.fna All virus genomes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	172 │ ├── input.phages_combined.gbk All virus genomes GenBank format file for .
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	173 │ ├── input.phages_combined.txt List of names (FASTA definition lines) for all virus genomes.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	174 │ ├── input.phages_lysogenic.faa Virus encoded proteins for predicted lysogenic viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	175 │ ├── input.phages_lysogenic.ffn Virus encoded genes for predicted lysogenic viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	176 │ ├── input.phages_lysogenic.fna Virus genomes for predicted lysogenic viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	177 │ ├── input.phages_lytic.faa Virus encoded proteins for predicted lytic viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	178 │ ├── input.phages_lytic.ffn Virus encoded genes for predicted lytic viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	179 │ └── input.phages_lytic.fna Virus genomes for predicted lytic viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	180 └── VIBRANT_results_input Folder containing useful tab-delimited files for predicted viruses.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	181 ├── VIBRANT_AMG_counts_input.tsv List of all predicted virus AMGs (by KEGG KO) and the total number of each. Summary of file VIBRANT_AMG_individuals_input
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	182 ├── VIBRANT_AMG_individuals_input.tsv List of individual predicted virus AMGs by protein and its respective genome. AMGs are determined by KEGG annotation but Pfam annotation is also given if applicable.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	183 ├── VIBRANT_AMG_pathways_input.tsv List summarizing the present KEGG metabolic pathways (by KEGG map entry) corresponding to virus AMGs.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	184 ├── VIBRANT_annotations_input.tsv 38 Complete list of annotations and associated information for KEGG, Pfam and VOG for all predicted viruses.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	185 ├── VIBRANT_complete_circular_input.tsv 39 Virus genomes that were predicted to be circular and therefore complete genomes.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	186 ├── VIBRANT_figure_PCA_input.tsv 40 Coordinate information for each viral scaffold on the PCA plot
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	187 ├── VIBRANT_genbank_table_input.tsv 41 List of the single annotation used for all predicted virus proteins. Annotations are chosen based on best score hit.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	188 ├── VIBRANT_genome_quality_input.tsv 42 List summarizing the predicted genome quality and type (lytic/lysogenic) for all predicted viruses.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	189 ├── VIBRANT_integrated_prophage_coordinates_input.tsv 43 Scaffold/genome coordinate information of each integrated provirus that was excised from a host scaffold.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	190 ├── VIBRANT_machine_input.tsv 44 List summarizing predictions made by the neural network machine learning classifier.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	191 ├── VIBRANT_summary_normalized_input.tsv 45 Normalized version of file VIBRANT_summary_results_input
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	192 └── VIBRANT_summary_results_input.tsv 46 List of complete annotation summary metrics for each predicted virus genome. -->
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	193 </outputs>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	194 <tests>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	195 <!-- Tests for vibrant are commented. To run them
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	196 - uncomment test
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	197 - download-db.sh tools/vibrant/test-data/db/ -->
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	198 <!-- <test expect_num_outputs="4">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	199 <param name="input" value="mixed_example.fasta"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	200 <param name="database" value="test"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	201 <output_collection name="figures" count="5"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	202 <output name="phages_combined_fna">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	203 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	204 <has_text text=">" n="4"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	205 <has_n_lines n="8"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	206 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	207 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	208 <output name="phages_combined_txt">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	209 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	210 <has_n_lines n="4"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	211 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	212 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	213 <output name="phages_combined_gbk">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	214 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	215 <has_line line="//" n="3"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	216 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	217 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	218 </test>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	219 <test expect_num_outputs="25">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	220 <param name="input" value="mixed_example.fasta"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	221 <param name="database" value="test"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	222 <param name="outputs" value="figures,phages_circular_fna,phages_combined_faa,phages_combined_ffn,phages_combined_fna,phages_combined_gbk,phages_combined_txt,phages_lysogenic_faa,phages_lysogenic_ffn,phages_lysogenic_fna,phages_lytic_faa,phages_lytic_ffn,phages_lytic_fna,AMG_counts,AMG_individuals,AMG_pathways,annotations,complete_circular,figure_PCA,genbank_table,genome_quality,integrated_prophage_coordinates,machine,summary_normalized,summary_results"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	223 <output_collection name="figures" count="5"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	224 <output name="phages_combined_fna">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	225 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	226 <has_text text=">" n="4"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	227 <has_n_lines n="8"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	228 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	229 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	230 <output name="phages_combined_txt">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	231 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	232 <has_n_lines n="4"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	233 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	234 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	235 <output name="annotations">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	236 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	237 <has_n_lines n="146"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	238 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	239 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	240 <output name="phages_combined_gbk">
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	241 <assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	242 <has_line line="//" n="3"/>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	243 </assert_contents>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	244 </output>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	245 </test> -->
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	246 </tests>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	247 <help><![CDATA[
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	248
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	249 .. class:: infomark
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	250
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	251 What it does
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	252
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	253 VIBRANT is a tool for automated recovery and annotation of bacterial and
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	254 archaeal viruses, determination of genome completeness, and characterization of
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	255 viral community function from metagenomic assemblies. VIBRANT uses neural
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	256 networks of protein annotation signatures and genomic features to maximize
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	257 identification of highly diverse partial or complete viral genomes as well as
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	258 excise integrated proviruses.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	259
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	260 - Uses neural network machine learning of protein annotation signatures
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	261 - Asigns novel 'v-score' for determining the virus-like nature of all annotations
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	262 - Determines genome completeness
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	263 - Characterizes viral community function by metabolic analysis
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	264 - Identifies auxiliary metabolic genes (AMGs)
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	265 - Excises integrated viral genomes from host scaffolds
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	266 - Performs well in diverse environments
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	267 - Recovers novel and abundant viral genomes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	268 - Built for dsDNA, ssDNA and RNA viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	269
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	270 VIBRANT uses three databases for identifying viruses and characterizing virome metabolic potential:
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	271
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	272 - KEGG (March release): https://www.genome.jp/kegg/ (FTP: ftp://ftp.genome.jp/pub/db/kofam/archives/2019-03-20/)
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	273 - Pfam (v32): https://www.ebi.ac.uk/interpro/ (FTP: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/)
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	274 - VOG (release 94): http://vogdb.org/ (FTP: http://fileshare.csb.univie.ac.at/vog/vog94/)
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	275
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	276 Usage
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	277 .....
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	278
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	279 Input
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	280
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	281 FASTA formated nucleotide or amino acid sequences. Note that for amino acid
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	282 input Input is protein needs to be checked.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	283
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	284 Output
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	285
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	286 Run log file: Contains information about the command used, the total runtime,
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	287 date of run, version of VIBRANT, and summary of values used in the figure
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	288 dataset phages. This log ﬁle is more of a run and output summary dataset, though
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	289 in the event of an error the message will be displayed in this log dataset.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	290
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	291 Figures:
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	292
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	293 - pathways: bar plot of KEGG pathways for identified viral AMGs
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	294 - PCA: principal component analysis of predicted viruses, contains information
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	295 on quality, lifestyle, circular/linear, size and general relationships of viral
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	296 scaffolds. A PCA plot will only be generated if at least 3 viral scaffolds are
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	297 identified. Based on the Normalized summary metrics output dataset and
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	298 Scaffold coordinates on the PCA plot provides coordinate information for each
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	299 scaffold.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	300 - phages: Nested bubble plot for ratio of total input scaffolds (outside),
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	301 number of scaffolds that were greater than or equal to minimum size restrictions
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	302 (middle), and number of identified viruses (inside). Must have at least 10 input
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	303 sequences for this file to be present. The represented numbers can be found in
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	304 the run log file.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	305 - quality: bar plot of number of viruses per genome quality category. Possible
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	306 x-axis categories are high, medium and low quality draft, and complete
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	307 circular. Any category may not be present if no viruses were identified for that
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	308 category.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	309 - sizes: histogram of genome sizes of identified viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	310
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	311 FASTA and associated files for predicted viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	312
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	313 - Circular virus genomes: All virus genomes identified as circular
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	314 - Virus encoded protein: All virus encoded proteins. Note: any lysogenic virus
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	315 that has been excised from a host scaffold will have the term "fragment" and a
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	316 number appended to the original name to indicate that it does not represent the
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	317 entire scaffold. This file () will contain only the excised fragment.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	318 - Virus encoded genes: All virus encoded genes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	319 - Virus genomes: All virus genomes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	320 - Virus genomes genbank: GenBank format file for all virus genomes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	321 - Virus genome names: List of names (FASTA definition lines) for all virus
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	322 genomes. Note: This file may not entirely match the original input sequence
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	323 names due to fragmentation of scaﬀolds.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	324 - Lysogenic/Lytic virus encoded proteins: Virus encoded proteins for predicted lysogenic/lytic viruses (subset of the above datasets).
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	325 - Lysogenic/Lytic virus encoded gene: Virus encoded genes for predicted lysogenic/lytic viruses (subset of the above datasets).
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	326 - Lysogenic/Lytic virus genomes: Virus genomes for predicted lysogenic/lytic viruses (subset of the above datasets).
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	327
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	328 Useful tab-delimited files for predicted viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	329
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	330 - Predicted virus AMGs: List of all predicted virus AMGs (by KEGG KO) and the
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	331 total number of each. Summary of file Individual predicted virus AMGs. File
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	332 may be empty.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	333 - Individual predicted virus AMGs: List of individual predicted virus AMGs by
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	334 protein and its respective genome. AMGs are determined by KEGG annotation but
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	335 Pfam annotation is also given if applicable. See file Predicted virus AMGs for
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	336 summary. File may be empty.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	337 - KEGG metabolic pathways corresponding to virus AMGs: List summarizing the
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	338 present KEGG metabolic pathways (by KEGG map entry) corresponding to virus AMGs.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	339 See dataset Individual predicted virus AMGs for individual AMGs. File may be
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	340 empty. See this link for detailed information regarding KEGG metabolic pathways:
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	341 https://www.genome.jp/kegg/pathway.html.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	342 - Annotations for KEGG, Pfam and VOG: Complete list of annotations and
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	343 associated information for KEGG, Pfam and VOG for all predicted viruses.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	344
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	345 - Blank rows indicate proteins that were not given an annotation.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	346 - Annotation names can be found in columns KO/KO name, Pfam/Pfam name and VOG/VOG name.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	347 - Column AMG will indicate if the annotation was considered an AMG or not (blank).
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	348 - Columns for evalue and score refer to the annotation confidences generated
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	349 by HMMsearch. Evalues are provided, but scores are used as the cutoff for
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	350 annotations (must have a score of at least 40).
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	351 - Columns for v-score refer to the VIBRANT-specific virus-like score
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	352 associated with each KO, Pfam and VOG. Briefly: scores of
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	353
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	354 - 0 indicate very low or no relatedness to viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	355 - 0.01 - 0.1 indicates low relatedness;
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	356 - 0.1 - 1 indicates moderate relatedness;
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	357 - 1 - 5 indicates significant relatedness;
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	358 - 5 - 10 indicates substantial relatedness;
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	359 - 10 (max) for most cases indicates viral hallmark genes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	360
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	361 - Complete circular genomes: Virus genomes that were predicted to be circular
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	362 and therefore complete genomes. File may be empty. Circularization is determined
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	363 by a kmer-based search between each end of the viral predicted genome. There
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	364 must be at least a 20bp identical match.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	365 - Scaffold coordinates on the PCA plot: Coordinate information for each viral scaffold on the PCA plot
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	366 - Single annotation used for all predicted virus proteins: List of the single
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	367 annotation used for all predicted virus proteins. Annotations are chosen based
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	368 on best score hit. This dataset is used to generate dataset Virus genomes
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	369 - Predicted genome quality and type: List summarizing the predicted genome
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	370 quality and type (lytic/lysogenic) for all predicted viruses. Qualities may be
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	371 fragment, low, medium or high quality draft. Complete circular genomes, if
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	372 applicable, are listed at the end and are redundant. That is, any complete
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	373 circular genome will also be given a quality.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	374 - Coordinates of integrated provirus: Scaffold/genome coordinate information of
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	375 each integrated provirus that was excised from a host scaffold. This dataset
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	376 provides the location of the putative provirus by both protein and nucleotide
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	377 coordinates. All viral scaffolds are respective of those with "fragment\_" in the
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	378 name.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	379 - Predictions of the neural network classifier: List summarizing predictions
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	380 made by the neural network machine learning classiﬁer. Will contain both viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	381 and nonviruses. This dataset is likely not of use but can be informative for
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	382 checking outputs. There are curation steps following the classiifer to validate
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	383 predictions, so predictions in this file may not exactly match the final output.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	384 File may be empty if the classiﬁer was not used.
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	385 - Normalized summary metrics: Normalized version of the Summary metrics
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	386 dataset. This normalized version was used to construct the PCA plot and is also
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	387 the data read into the neural network classifier. Total proteins per scaffold
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	388 are normalized as log10 of total proteins, and all other metrics per scaffold
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	389 are normalized by dividing the original metric by the original number of encoded
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	390 proteins
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	391 - Summary metrics: List of complete annotation summary metrics for each
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	392 predicted virus genome. The most useful metrics will be columns 1 through 8. All
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	393 metrics shown, if applicable, were used for the neural network machine learning
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	394 classifier. Explanations of each column:
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	395
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	396 - scaffold: the name of the predicted virus
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	397 - total genes: total number of predicted open reading frames
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	398 - all KEGG: total number of KEGG annotations
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	399 - KEGG v-score: sum of all KEGG annotation v-scores
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	400 - all Pfam: total number of Pfam annotations
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	401 - Pfam v-score: total number of Pfam annotations
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	402 - all VOG: total number of VOG annotations
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	403 - VOG v-score: total number of VOG annotations
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	404 - KEGG int-rep: total number of KEGG integration related annotations (e.g., integrase, replicase, transposase). Useful for separating plasmids, mobile genetic elements and viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	405 - KEGG zero: total number of KEGG annotations that had a v-score of zero
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	406 - Pfam int-rep: total number of Pfam integration related annotations (e.g., integrase, replicase, transposase). Useful for separating plasmids, mobile genetic elements and viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	407 - Pfam zero: total number of KEGG annotations that had a v-score of zero
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	408 - VOG redoxin: total number of VOG redoxin related annotations (e.g., glutaredoxin, thioredoxin). Useful for separating viruses from bacteria/archaea because redoxins are common amongst viruses and therefore are given a high v-score, but are also common amongst bacteria/archaea
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	409 - VOG rec-tran: total number of VOG integration related annotations that are not integrase (e.g., replicase, transposase). Useful for separating plasmids, mobile genetic elements and viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	410 - VOG int: total number of VOG integrase related annotations. Used to identify putative lysogenic viruses. Also useful for separating plasmids, mobile genetic elements and viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	411 - VOG RnR: total number of VOG ribonucleotide reductase (RnR) related annotations. Useful for separating viruses from bacteria/archaea because RnRs are common amongst viruses and therefore are given a high v-score, but are also common amongst bacteria/archaea
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	412 - VOG DNA: total number of VOG nucleotide (DNA/RNA) replication related annotations. Useful for separating viruses from bacteria/archaea because nucleotide replication proteins are common amongst viruses and therefore are given a high v-score, but are also common amongst bacteria/archaea. This is also a metric used for predicting viral completeness (along with VOG special) because genome replication is an essential process
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	413 - KEGG restriction: total number of KEGG restriction nuclease related annotations. Useful for separating plasmids, mobile genetic elements and viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	414 - KEGG toxin: total number of KEGG toxin/anti-toxin related annotations. Useful for separating plasmids, mobile genetic elements and viruses
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	415 - VOG special: total number of VOG hallmark annotations (e.g., virion structural proteins, holin/lysin, terminase). This is a metric used for predicting viral completeness (along with VOG DNA)
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	416 - annotation check: the number of proteins annotated by KEGG, Pfam and VOG
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	417 - p\_v check: the number of proteins annotated by Pfam and VOG only
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	418 - p\_k check: the number of proteins annotated by KEGG and Pfam only
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	419 - k\_v check: the number of proteins annotated by KEGG and VOG only
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	420 - k check: the number of proteins annotated by KEGG only
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	421 - p check: the number of proteins annotated by Pfam only
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	422 - v check: the number of proteins annotated by VOG only
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	423 - h check: the number of proteins not annotated
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	424
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	425 ]]></help>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	426 <citations>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	427 <citation type="doi">10.1186/s40168-020-00867-0</citation>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	428 </citations>
b238f5afa054 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/vibrant commit b4b2e3d4bfdb4f4db027f7131e83fa3a6e65aca2 ufz parents: diff changeset	429 </tool>

Mercurial > repos > ufz > vibrant

annotate vibrant.xml @ 1:353fc14d89aa draft default tip