# HG changeset patch
# User ximgchess
# Date 1681295286 0
# Node ID 47a0648cdfd146a5e9f0bcb3699284fa9221ad1b
# Parent  ed26d2bb9723f3237ab6f39852bae27bf991e641
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3e8c1c54d5e12fdbc4f6c5cdae88b6d054db7c45

diff -r ed26d2bb9723 -r 47a0648cdfd1 tomo/.tomo_reduce.xml.swp
Binary file tomo/.tomo_reduce.xml.swp has changed
diff -r ed26d2bb9723 -r 47a0648cdfd1 tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Tue Apr 11 20:02:52 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 10:28:06 2023 +0000
@@ -6,20 +6,7 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        mkdir tomo_reduce_plots;
-        pip --exists-action i install certif-pyspec==1.5.3 &&
-        #if str($map.type_selector) == "YAML"
-            cp '$input_file' map.yaml &&
-        #else
-            cp '$input_file' setup.nex &&
-        #end if
-        cp '$tool_config' reduce.yaml &&
-        CHAP --config 
-        #if str($map.type_selector) == "YAML"
-            '$__tool_directory__/pipeline_reduce_yaml.yaml'
-        #else
-            '$__tool_directory__/pipeline_reduce_nexus.yaml'
-        #end if
+            cp '$input_file' output.yaml
         ]]>
     </command>
     <configfiles>
@@ -75,11 +62,14 @@
         </conditional>
     </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"/>
+        -->
+        <data name="output_file" format="yaml" label="Test output" from_work_dir="output.yaml"/>
     </outputs>
     <help>
         <![CDATA[