Mercurial > repos > ximgchess > chap_test_20230411

changeset 48:ec5a7fc248d6 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty
author ximgchess
date Wed, 12 Apr 2023 15:03:22 +0000
parents d53ca5ae6e76
children 7df62c196577
files tomo/tomo_reduce.xml
diffstat 1 files changed, 3 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/tomo/tomo_reduce.xml	Wed Apr 12 14:39:31 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 15:03:22 2023 +0000
@@ -6,20 +6,9 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-        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
+        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
         ]]>
     </command>
     <configfiles>