Mercurial > repos > ximgchess > chap_test_20230411

diff tomo/tomo_reduce.xml @ 83:9b6e931e0de0 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty
author ximgchess
date Tue, 02 May 2023 15:07:28 +0000
parents 6b20bd5d489a
children 1e02b5c4abdf
line wrap: on
line diff
--- a/tomo/tomo_reduce.xml	Mon May 01 13:16:34 2023 +0000
+++ b/tomo/tomo_reduce.xml	Tue May 02 15:07:28 2023 +0000
@@ -6,7 +6,21 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3'
+        mkdir tomo_reduce_plots;
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
+            cp $input_file map.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
+        #end if
         ]]>
     </command>
     <configfiles>