# HG changeset patch
# User ximgchess
# Date 1681315587 0
# Node ID 05984baac64e06332a5d23e39d73e22c683694e5
# Parent  7df62c1965778413821fc71bc12daf0f31764d31
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

diff -r 7df62c196577 -r 05984baac64e tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Wed Apr 12 15:10:24 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 16:06:27 2023 +0000
@@ -6,20 +6,8 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        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
+        which python
+        cp $tool_config reduce.yaml &&
         ]]>
     </command>
     <configfiles>
@@ -79,10 +67,6 @@
     </inputs>
     <outputs>
         <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
-        <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
-            <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
-        </collection>
-        <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
     </outputs>
     <help>
         <![CDATA[