diff tomo/tomo_reduce.xml @ 60:3a9135044f14 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

--- a/tomo/tomo_reduce.xml	Wed Apr 12 18:58:32 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 19:04:05 2023 +0000
@@ -6,20 +6,26 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
+        mkdir tomo_reduce_plots;
         $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
-        ls -alh $__tool_directory__/.. &&
-        cp $tool_config reduce.yaml
+        #if str($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
+            $__tool_directory__/pipeline_reduce_nexus.yaml
+        #end if
         ]]>
     </command>
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
-#*
-#if str($map.type_selector) == "yaml"
-#echo 'detector:' #
-#echo '  file: ' + str($__tool_directory__) + '/andor2.yaml' #
-#end if
-*#
 #echo 'img_x_bounds:' #
 #if str($img_x_bounds.type_selector) == "full_range"
 #echo '- -1' #
@@ -68,6 +74,10 @@
     </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[