Mercurial > repos > ximgchess > chap_test_20230411

diff tomo/tomo_reduce.xml @ 79:7638a2c68b7f draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
author ximgchess
date Mon, 01 May 2023 12:50:46 +0000
parents d0bc5f9dc4c9
children 1cfbaaec71aa
line wrap: on
line diff
--- a/tomo/tomo_reduce.xml	Thu Apr 27 11:01:04 2023 +0000
+++ b/tomo/tomo_reduce.xml	Mon May 01 12:50:46 2023 +0000
@@ -10,16 +10,10 @@
         $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
         #if str($map.type_selector) == "yaml"
             cp $input_file map.yaml &&
-            cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
+            cat $__tool_directory__/$map.detector.type_selector $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>
@@ -51,9 +45,9 @@
                         <option value="manta.yaml">manta</option>
                         <option value="retiga.yaml">retiga</option>
                     </param>
-                    <when value="andor2"/>
-                    <when value="manta"/>
-                    <when value="retiga"/>
+                    <when value="andor2.yaml"/>
+                    <when value="manta.yaml"/>
+                    <when value="retiga.yaml"/>
                 </conditional>
             </when>
             <when value="nexus">