Mercurial > repos > ximgchess > chap_test_20230411

changeset 49:7df62c196577 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty
author ximgchess
date Wed, 12 Apr 2023 15:10:24 +0000
parents ec5a7fc248d6
children 05984baac64e
files tomo/tomo_reduce.xml
diffstat 1 files changed, 14 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/tomo/tomo_reduce.xml	Wed Apr 12 15:03:22 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 15:10:24 2023 +0000
@@ -6,9 +6,20 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        pip --exists-action i install --target /nfs/chess/galaxy-dev/var/dependencies/_conda/envs/mulled-v1-11c149728ce3e160bbcd143e6baec7605473b9b3f4d2da41f5e09a0cfb5db23f/lib/python3.10/site-packages certif-pyspec==1.5.3 &&
-        pip --exists-action i install --target /nfs/chess/galaxy-dev/var/dependencies/_conda/envs/mulled-v1-11c149728ce3e160bbcd143e6baec7605473b9b3f4d2da41f5e09a0cfb5db23f/lib/python3.10/site-packages pyfai==2023.3.0 3 &&
-        cp $tool_config reduce.yaml
+        mkdir tomo_reduce_plots;
+        #if str($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>