diff main_macros.xml @ 5:97be83fc3677 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 90f081e58b5ee41bba3a7e6f01d97b5bd9392759

--- a/main_macros.xml	Thu Feb 20 19:47:16 2025 +0000
+++ b/main_macros.xml	Wed May 28 21:14:59 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.5.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
 
     <xml name="vitessce_requirements">
@@ -68,6 +68,7 @@
             --inputs '$inputs'
             --output '${output.files_path}'
             --image '${output.files_path}/A/0/image01.ome.tiff'
+            --galaxy_config '${galaxy_config}'
             --offsets '$image.metadata.offsets'
             #if $masks
                 --masks '${output.files_path}/A/0/masks01.ome.tiff'
@@ -76,8 +77,9 @@
             --anndata '$anndata'
             #end if
             &&
-        cp '$__tool_directory__/index.html' '$output';
-        echo "export var config = \$(cat ${output.files_path}/config.json)" >> '${output.files_path}/config.js';
+        cp '$__tool_directory__/index.html' '$output' &&
+        sed -i 's|display?filename=/|display?filename=|g' ${output.files_path}/config.json &&
+        echo "export var config = \$(cat ${output.files_path}/config.json)" >> '${output.files_path}/config.js' &&
         cat '${output.files_path}/config.json' >> '$vitessce_config';
         ]]>
         </command>