Mercurial > repos > dfornika > render_tree
changeset 0:342fe8c2d8bb draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/render_tree commit 8898f2229ec13917b7d96e20725f3871d9d93e90-dirty
| author | dfornika |
|---|---|
| date | Sat, 29 Jun 2019 00:13:08 -0400 |
| parents | |
| children | 9f0241ee55e8 |
| files | render_tree.R render_tree.xml test-data/data.csv test-data/tree.nhx test-data/tree.png |
| diffstat | 5 files changed, 82 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/render_tree.R Sat Jun 29 00:13:08 2019 -0400 @@ -0,0 +1,18 @@ +#!/usr/bin/env Rscript + +suppressMessages( + library(ggtree) +) + +args = commandArgs(trailingOnly=TRUE) + +tree <- read.tree(args[1]) + +tree_plot <- ggplot(tree, aes(x, y)) + + geom_tree() + + theme_tree2() + + geom_tiplab() + +suppressMessages( + ggsave(args[2], plot=tree_plot, device="png") +)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/render_tree.xml Sat Jun 29 00:13:08 2019 -0400 @@ -0,0 +1,36 @@ +<tool id="render_tree" name="render tree" version="0.1.0"> + <description>render a newick tree</description> + <requirements> + <requirement type="package" version="1.16">bioconductor-ggtree</requirement> + </requirements> + <version_command>echo '0.1.0'</version_command> + <command detect_errors="exit_code"><![CDATA[ + $__tool_directory__/render_tree.R + '${tree}' + '${image}' + ]]></command> + <inputs> + <param name="tree" type="data" format="nhx" /> + </inputs> + <outputs> + <data name="image" format="png" /> + </outputs> + <tests> + </tests> + <help><![CDATA[ + ]]></help> + <citations> + <citation type="bibtex"> +@article{yu2017ggtree, + title={ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data}, + author={Yu, Guangchuang and Smith, David K and Zhu, Huachen and Guan, Yi and Lam, Tommy Tsan-Yuk}, + journal={Methods in Ecology and Evolution}, + volume={8}, + number={1}, + pages={28--36}, + year={2017}, + publisher={Wiley Online Library} +} + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.csv Sat Jun 29 00:13:08 2019 -0400 @@ -0,0 +1,9 @@ +taxa,number,fruit +A,1,apple +B,2,banana +C,3,carrot +D,4,date +E,5,eggplant +F,6,fruit +G,7,grape +H,8,honeydew \ No newline at end of file