# HG changeset patch
# User ximgchess
# Date 1681309559 0
# Node ID eef6fd51373659e71a2641a1ab4d1bd2bdd25cef
# Parent  d0d62ad6daa44f8a9bc0c04454d4331a3accbc09
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

diff -r d0d62ad6daa4 -r eef6fd513736 tomo/.tomo_reduce.xml.swp
Binary file tomo/.tomo_reduce.xml.swp has changed
diff -r d0d62ad6daa4 -r eef6fd513736 tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Wed Apr 12 14:22:57 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 14:25:59 2023 +0000
@@ -6,20 +6,13 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        mkdir tomo_reduce_plots;
         pip --exists-action i install --target='/nfs/chess/galaxy-dev/var/dependencies/_conda/envs' certif-pyspec==1.5.3
         #if str($map.type_selector) == "yaml"
             cp $input_file map.yaml &&
-            cat $__tool_directory__/andor2.yaml $tool_config > reduce.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
+            cp $tool_config reduce.yaml
         #end if
         ]]>
     </command>
@@ -80,10 +73,6 @@
     </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[