# HG changeset patch
# User iuc
# Date 1588674045 14400
# Node ID ef1c257adcbd933b1a11a339459ef4cce87cf2dc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
diff -r 000000000000 -r ef1c257adcbd drep_compare.xml
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+++ b/drep_compare.xml Tue May 05 06:20:45 2020 -0400
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+ compare a list of genomes
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+ macros.xml
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+ `_ performs rapid pair-wise comparison of genome sets.
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+`dRep compare `_ can rapidly and accurately compare a list of genomes in a pair-wise manner. This allows identification of groups of organisms that share similar DNA content in terms of Average Nucleotide Identity (ANI).
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+dRep performs this in two steps:
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+ - first with a rapid primary algorithm (Mash)
+ - second with a more sensitive algorithm (ANIm).
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+We can’t just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters `_ and `Module Descriptions `_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists.
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+dRep first compares all genomes using Mash, and then only runs the secondary algorithm (ANIm or gANI) on sets of genomes that have at least 90% Mash ANI. This results in a great decrease in the number of (slow) secondary comparisons that need to be run while maintaining the sensitivity of ANIm.
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+**INPUTS**
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+ - Genome sets in fasta format.
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+**OUTPUTS**
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+ - `Figures `_ that show the relationship of the Genome inputs.
+ - `Warnings `_ report two things: de-replicated genome similarity and secondary clusters that were almost different.
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+ ]]>
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diff -r 000000000000 -r ef1c257adcbd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue May 05 06:20:45 2020 -0400
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+ 2.5.4
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+ drep
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+ 10.1038/ismej.2017.126
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+ --ignoreGenomeQuality is useful with
+ bacteriophages or eukaryotes or things where checkM
+ scoring does not work. Will only choose genomes based
+ on length and N50.
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+ Using the checkm method of lineage_wf can require more than 40Gb of RAM.
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+ (for ANIn/ANImf only; gANI can only do larger method)
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+ (passed to scipy.cluster.hierarchy.linkage)
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+Based off of the formula:
+A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)
+A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight;
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+ (for ANIn/ANImf only; gANI can only do larger method)
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+ 'log' in select_outputs or not select_outputs
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+ 'warnings' in select_outputs
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+ 'Primary_clustering_dendrogram' in select_outputs
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+ 'Secondary_clustering_dendrograms' in select_outputs
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+ 'Secondary_clustering_MDS' in select_outputs
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+ 'Clustering_scatterplots' in select_outputs
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+ 'Cluster_scoring' in select_outputs
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+ 'Winning_genomes' in select_outputs
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+ 'Widb' in select_outputs
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+ 'Chdb' in select_outputs
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