# HG changeset patch
# User jjohnson
# Date 1578327066 18000
# Node ID b59ae99e47d4ed87df16c60c6e1804b53264360a
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/drep commit b155a1d533b7317ceb0ec642ffe3e986117df539"
diff -r 000000000000 -r b59ae99e47d4 drep_compare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/drep_compare.xml Mon Jan 06 11:11:06 2020 -0500
@@ -0,0 +1,59 @@
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+ compare a list of genomes
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+ macros.xml
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diff -r 000000000000 -r b59ae99e47d4 drep_dereplicate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/drep_dereplicate.xml Mon Jan 06 11:11:06 2020 -0500
@@ -0,0 +1,66 @@
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+ De-replicate a list of genomes
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+ macros.xml
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diff -r 000000000000 -r b59ae99e47d4 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jan 06 11:11:06 2020 -0500
@@ -0,0 +1,388 @@
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+ 2.3.2
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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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+ (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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