# HG changeset patch
# User azomics
# Date 1624485399 0
# Node ID ffc083c86d4448172c6ac78f5d606962e6a7f28a
# Parent  ca7ba337b7274bbf655d7c8462c6c4b34dc3a458
"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/flow_compensate commit fd7533e2c5c6c078bd2734c1ded95db9b74e450e"

diff -r ca7ba337b727 -r ffc083c86d44 flow-compensate.xml
--- a/flow-compensate.xml	Tue May 25 00:07:44 2021 +0000
+++ b/flow-compensate.xml	Wed Jun 23 21:56:39 2021 +0000
@@ -11,7 +11,7 @@
           ln -s '$fcs' input_dir/'$fcs.element_identifier';
         #end for 
         mkdir -p output_dir;
-        Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir
+        Rscript '$compensate_script' '$compensation_matrix' input_dir output_dir &> '$log_file'
       ]]></command>
     <configfiles>
       <configfile name="compensate_script"><![CDATA[
@@ -47,6 +47,7 @@
       <collection name="compensated_fcs" format="fcs" label="${tool.name} compensated FCS files on ${on_string}" type="list">
         <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
       </collection>
+      <data name="log_file" format="txt" label="Log for compensation by ${tool.name} on ${on_string}"/> 
     </outputs>
     <help><![CDATA[
         TODO: Fill in help.