# HG changeset patch
# User eschen42
# Date 1649123288 0
# Node ID 2b9119d7d80ae332d81c6f1e0b4157f299428dc8
# Parent  2c5f1a2fe16a8d9452591520f8aee33de78a8a6d
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227"

diff -r 2c5f1a2fe16a -r 2b9119d7d80a macros.xml
--- a/macros.xml	Sat Mar 26 02:27:12 2022 +0000
+++ b/macros.xml	Tue Apr 05 01:48:08 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.6</token>
+    <token name="@TOOL_VERSION@">0.1.7</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -13,7 +13,6 @@
             <requirement type="package" version="1.56.0"  >bioconductor-preprocesscore</requirement>
             <requirement type="package" version="1.64"    >perl-dbd-sqlite</requirement>
             <requirement type="package" version="1.7.1"   >r-optparse</requirement>
-            <requirement type="package" version="1.7.1"   >r-optparse</requirement>
             <requirement type="package" version="2.11"    >r-rmarkdown</requirement>
             <!--
             It would be nice to use conda-forge/texlive-core rather than r-tinytex because the
diff -r 2c5f1a2fe16a -r 2b9119d7d80a mqppep_anova.xml
--- a/mqppep_anova.xml	Sat Mar 26 02:27:12 2022 +0000
+++ b/mqppep_anova.xml	Tue Apr 05 01:48:08 2022 +0000
@@ -1,4 +1,10 @@
-<tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
+<tool
+  id="mqppep_anova"
+  name="MaxQuant Phosphopeptide ANOVA"
+  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+  python_template_version="3.5"
+  profile="21.05"
+  >
     <description>Perform ANOVA on merged and filtered data from phospho-peptide enrichment/MaxQuant pipeline</description>
     <macros>
         <import>macros.xml</import>
@@ -10,16 +16,15 @@
       biocontainer are read-only, so this builds a pseudo-home under /tmp
     -->
     <command detect_errors="exit_code"><![CDATA[
-      export OLD_PWD=\$(dirname \$(pwd));
-      export HOME=/tmp\${OLD_PWD};
-      mkdir -p \$HOME/bin;
-      mkdir -p \$HOME/tmp;
-      export TEMP=\$HOME/tmp;
-      export TMPDIR=\$TEMP;
-      cd \$TEMP;
+      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;
-      \${CONDA_PREFIX}/bin/Rscript \$TEMP/mqppep_anova.R
+      Rscript \${HOME}/mqppep_anova.R
         --inputFile '$input_file'
         --alphaFile '$alpha_file'
         --firstDataColumn $intensity_column_regex_f
@@ -34,8 +39,6 @@
         --imputedQNLTDataFile '$imp_qn_lt_file'
         --reportFile '$report_file';
       export RESULT=\$?;
-      cd \${OLD_PWD};
-      rm -rf \$HOME;
       exit \${RESULT}
     ]]></command>
     <configfiles>