Mercurial > repos > eschen42 > mqppep_anova

diff mqppep_anova.xml @ 17:bb38aac026b9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aea9ac5a98069c3c993bd7903eda732f8ae2109d"
author eschen42
date Wed, 06 Apr 2022 05:48:05 +0000
parents 2b9119d7d80a
children 61adb8801b73
line wrap: on
line diff
--- a/mqppep_anova.xml	Tue Apr 05 01:48:08 2022 +0000
+++ b/mqppep_anova.xml	Wed Apr 06 05:48:05 2022 +0000
@@ -16,15 +16,9 @@
       biocontainer are read-only, so this builds a pseudo-home under /tmp
     -->
     <command detect_errors="exit_code"><![CDATA[
-      export HOME=\${_GALAXY_JOB_HOME_DIR};
-      export TEMP=\${_GALAXY_JOB_TMP_DIR};
-      export TMPDIR=\${TEMP};
-      mkdir -p \${HOME}/bin;
-      mkdir -p \${HOME}/tmp;
-      cd \${HOME};
       cp '$__tool_directory__/mqppep_anova_script.Rmd' . || exit 0;
-      cp '$__tool_directory__/mqppep_anova.R' . || exit 0;
-      Rscript \${HOME}/mqppep_anova.R
+      cp '$__tool_directory__/mqppep_anova.R'          . || exit 0;
+      Rscript mqppep_anova.R
         --inputFile '$input_file'
         --alphaFile '$alpha_file'
         --firstDataColumn $intensity_column_regex_f