diff tomo/tomo_reduce.xml @ 61:a560d5143348 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty

--- a/tomo/tomo_reduce.xml	Wed Apr 12 19:04:05 2023 +0000
+++ b/tomo/tomo_reduce.xml	Thu Apr 13 12:18:11 2023 +0000
@@ -7,33 +7,32 @@
     <command detect_errors="exit_code">
         <![CDATA[
         mkdir tomo_reduce_plots;
-        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
-        #if str($map.type_selector) == "yaml"
-            cp $input_file map.yaml &&
-            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
+        pip --exists-action i install certif-pyspec==1.5.3 &&
+        #if str($map.type_selector) == "YAML"
+            cp '$input_file' map.yaml &&
         #else
-            cp $input_file setup.nex &&
-            cp $tool_config reduce.yaml &&
+            cp '$input_file' setup.nex &&
         #end if
+        cp '$tool_config' reduce.yaml &&
         CHAP --config 
-        #if str($map.type_selector) == "yaml"
-            $__tool_directory__/pipeline_reduce_yaml.yaml
+        #if str($map.type_selector) == "YAML"
+            '$__tool_directory__/pipeline_reduce_yaml.yaml'
         #else
-            $__tool_directory__/pipeline_reduce_nexus.yaml
+            '$__tool_directory__/pipeline_reduce_nexus.yaml'
         #end if
         ]]>
     </command>
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
-#echo 'img_x_bounds:' #
-#if str($img_x_bounds.type_selector) == "full_range"
-#echo '- -1' #
-#echo '- -1' #
-#else
-#echo '- ' + str($img_x_bounds.low) #
-#echo '- ' + str($img_x_bounds.upp) #
-#end if
+                #echo 'img_x_bounds:' #
+                #if str($img_x_bounds.type_selector) == "full_range"
+                    #echo '- -1'
+                    #echo '- -1'
+                #else
+                    #echo '- ' + str($img_x_bounds.low)
+                    #echo '- ' + str($img_x_bounds.upp)
+                #end if
             ]]>
         </configfile>
     </configfiles>