# HG changeset patch
# User ximgchess
# Date 1681310371 0
# Node ID d53ca5ae6e764b4f9bc82c0570e476d03d7b36ff
# Parent  b0487ea8333916aed1a387e3e9ae529d3589d4ed
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

diff -r b0487ea83339 -r d53ca5ae6e76 tomo/.tomo_reduce.xml.swp
Binary file tomo/.tomo_reduce.xml.swp has changed
diff -r b0487ea83339 -r d53ca5ae6e76 tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Wed Apr 12 14:38:09 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 14:39:31 2023 +0000
@@ -6,8 +6,20 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        pip --exists-action i install --target='/nfs/chess/galaxy-dev/var/dependencies/_conda/envs' pyfai==2023.3.0 &&
-        cp $tool_config reduce.yaml
+        mkdir tomo_reduce_plots;
+        #if str($map.type_selector) == "yaml"
+            cp $input_file map.yaml &&
+            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
+        #else
+            cp $input_file setup.nex &&
+            cp $tool_config reduce.yaml &&
+        #end if
+        CHAP --config 
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/pipeline_reduce_yaml.yaml
+        #else
+            $__tool_directory__/pipeline_reduce_nexus.yaml
+        #end if
         ]]>
     </command>
     <configfiles>