# HG changeset patch
# User ximgchess
# Date 1681309868 0
# Node ID 5d3313dbb8a225266646f51a09dc079577efbc1d
# Parent  7c2b2bb53c231b0d8a3ae330b6ee21d2ef61d4e9
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

diff -r 7c2b2bb53c23 -r 5d3313dbb8a2 tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Wed Apr 12 14:28:25 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 14:31:08 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 certif-pyspec==1.5.3 &&
-        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>
@@ -67,6 +79,10 @@
     </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[