# HG changeset patch
# User azomics
# Date 1594077764 14400
# Node ID 04afe468b2342cc3d64f7efb72fc8d8ecb3ab18f
# Parent  8e568997abdaa12232e15a900ce22c71e79e24e4
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_merge_downsample commit d62d7d86dafd09575d91ddb6d07a8dd6a6dc4a27"

diff -r 8e568997abda -r 04afe468b234 FCSMergeDownsample.xml
--- a/FCSMergeDownsample.xml	Mon Jun 22 20:35:09 2020 -0400
+++ b/FCSMergeDownsample.xml	Mon Jul 06 19:22:44 2020 -0400
@@ -1,15 +1,17 @@
-<tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1">
+<tool id="fcs_merge_downsample" name="Merge and downsample" version="1.0+galaxy1" profile="18.01">
   <description>FCS files with FlowSOM</description>
   <requirements>
     <requirement type="package" version="1.18.0">bioconductor-flowsom</requirement>
   </requirements>
   <stdio>
+    <exit_code range="1:9" level="fatal" description="See stderr for more details." />
     <exit_code range="10" level="fatal" description="One or more FCS files is not valid. See stderr for more details." />
     <exit_code range="11" level="fatal" description="Please provide a numeric value [0,1] for the downsampling factor." />
     <exit_code range="12" level="fatal" description="There are inconsistencies in marker names between FCS files." />
+    <exit_code range="13:" level="fatal" description="See stderr for more details." />
   </stdio>
   <command><![CDATA[
-      FCSMergeDownsample.R '${output_file}' '${outformat}' '${factorDS}'
+      Rscript --slave --vanilla '$__tool_directory__/FCSMergeDownsample.R' '${output_file}' '${outformat}' '${factorDS}'
   #for $f in $input
     '${f}'
   #end for