| Previous changeset 2:5892927664be (2019-02-26) Next changeset 4:994c509873db (2019-04-03) |
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Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93 |
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modified:
macros.xml |
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added:
dccm.R test-data/DCCM_raw_data.csv test-data/dccm_plot.png |
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| diff -r 5892927664be -r ddef4de91df6 dccm.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dccm.R Wed Mar 27 15:15:54 2019 -0400 |
| [ |
| @@ -0,0 +1,46 @@ +#!/usr/bin/env Rscript + +options(stringAsfactors = FALSE) +args <- commandArgs(trailingOnly = TRUE) + +library(bio3d) +require(lattice) + +dcdfile <- args[1] +pdbfile <- args[2] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + +selection <- args[3] +domain <- args[4] + +output <- args[5] +dccm_plot <- args[6] + +dcd <- read.dcd(dcdfile) +pdb <- read.pdb(pdbfile) + +if (selection == "string") { + inds <- atom.select(pdb, string = domain) +} +if (selection == "elety") { + inds <- atom.select(pdb, elety = domain) +} +if (selection == "resid") { + inds <- atom.select(pdb, resid = domain) +} +if (selection == "segid") { + inds <- atom.select(pdb, segid = domain) +} + +xyz <- fit.xyz(fixed=pdb$xyz, mobile=dcd, fixed.inds=inds$xyz, mobile.inds=inds$xyz) +cij<-dccm(xyz[,inds$xyz]) + +write.table(cij, file = output, row.names = TRUE, col.names = FALSE, quote =FALSE, sep="\t") + +png(dccm_plot) +plot(cij) +dev.off() + + |
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| diff -r 5892927664be -r ddef4de91df6 macros.xml --- a/macros.xml Tue Feb 26 08:27:55 2019 -0500 +++ b/macros.xml Wed Mar 27 15:15:54 2019 -0400 |
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| @@ -3,8 +3,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="2.3_3">r-bio3d</requirement> - <requirement type="package" version="1.16">r-ncdf4</requirement> - <requirement type="package" version="0.20_35">r-lattice</requirement> + <requirement type="package" version="0.20_35">r-lattice </requirement> <yield/> </requirements> </xml> @@ -20,6 +19,7 @@ </xml> <xml name="citations"> <citations> + <citation type="doi">10.1093/bioinformatics/btz107</citation> <citation type="doi">10.1093/bioinformatics/btl461</citation> </citations> </xml> |
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| diff -r 5892927664be -r ddef4de91df6 test-data/DCCM_raw_data.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DCCM_raw_data.csv Wed Mar 27 15:15:54 2019 -0400 |
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| b'@@ -0,0 +1,433 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| diff -r 5892927664be -r ddef4de91df6 test-data/dccm_plot.png |
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| Binary file test-data/dccm_plot.png has changed |
