Mercurial > repos > devteam > xy_plot
changeset 4:ecb437f1d298 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit d792f43f02cd0d6ab74411c21e0897937cb075aa
| author | devteam |
|---|---|
| date | Sun, 17 Dec 2017 12:37:44 -0500 |
| parents | 319fa5a9fc1b |
| children | |
| files | r_wrapper.sh tool_dependencies.xml xy_plot.xml |
| diffstat | 3 files changed, 2 insertions(+), 32 deletions(-) [+] |
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--- a/r_wrapper.sh Wed Dec 07 18:29:23 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -#!/bin/sh - -### Run R providing the R script in $1 as standard input and passing -### the remaining arguments on the command line - -# Function that writes a message to stderr and exits -function fail -{ - echo "$@" >&2 - exit 1 -} - -# Ensure R executable is found -which R > /dev/null || fail "'R' is required by this tool but was not found on path" - -# Extract first argument -infile=$1; shift - -# Ensure the file exists -test -f $infile || fail "R input file '$infile' does not exist" - -# Invoke R passing file named by first argument to stdin -R --vanilla --slave $* < $infile
--- a/tool_dependencies.xml Wed Dec 07 18:29:23 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="2.11.0"> - <repository changeset_revision="5824d2b3bc8b" name="package_r_2_11_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/xy_plot.xml Wed Dec 07 18:29:23 2016 -0500 +++ b/xy_plot.xml Sun Dec 17 12:37:44 2017 -0500 @@ -1,10 +1,9 @@ <tool id="XY_Plot_1" name="Plotting tool" version="1.0.2"> <description>for multiple series and graph types</description> <requirements> - <requirement type="package" version="3.2.1">R</requirement> - <requirement type="package" version="2.11.1">fontconfig</requirement> + <requirement type="package" version="3.4.2">r-base</requirement> </requirements> - <command interpreter="bash">r_wrapper.sh $script_file</command> + <command>Rscript $script_file</command> <configfiles> <configfile name="script_file"> ## Setup R error handling to go to stderr