diff macros.xml @ 1:579538ff939d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 5b54fc7af13196445abda407054e01dd3e5603c6

--- a/macros.xml	Thu Aug 11 13:50:09 2022 +0000
+++ b/macros.xml	Mon Jul 31 15:23:29 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.2</token>
+    <token name="@TOOL_VERSION@">0.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="biotools">
@@ -18,34 +18,28 @@
         <version_command>echo @TOOL_VERSION@</version_command>
     </xml>
     <xml name="vocdir_input">
-        <conditional name="vocdir_option">
+        <conditional name="voc_source">
             <param name="choice" type="select"
-                   label="Source of YAML files with definition of the variant of concerns"
-                   help="Cojac ships with a directory with variant definitions yaml files (https://github.com/cbg-ethz/cojac/tree/master/voc), which the tool can access internally. You can also download the latest version of the yaml files from https://github.com/phe-genomics/variant_definitions and use it as a custom yamls defining the variant of concerns.">
-                <option value="cache">Definitions shipped with the tool (can be outdated)</option>
-                <option value="custom">From history</option>
+                   label="Source of lineage definitions"
+                   help="Cojac detects lineage evidence based on lineage mutation patterns deined in tool-specific yaml format. You can choose between the (possibly outdated) definitions shipped with the tool or definitions provided as a collection of yaml datasets in your history. See the tool help below for more details.">
+                <option value="builtin">Lineage definitions shipped with the tool</option>
+                <option value="custom">YAML dataset collection in history</option>
             </param>
-            <when value="cache"/>
+            <when value="builtin"/>
             <when value="custom">
-                <param name="voc_file" type="data" format="yaml" multiple="true"
-                       label="YAML defining the variant of concern"/>
+                <param name="collection" type="data_collection" collection_type="list" format="yaml" label="Collection of lineage definitions" />
             </when>
         </conditional>
     </xml>
     <token name="@VOCDIR_COMMAND@"><![CDATA[
-#if $vocdir_option.choice == 'custom'
-    #set vocdir = 'voc/'
-    #set file_paths1 = []
+#if $voc_config.choice == 'custom'
     mkdir -p voc &&
-    #for $input_file in $voc_file
-        #set $file_path = $vocdir + $input_file.element_identifier
-        ln -s '$input_file' '$file_path' &&
-        $file_paths1.append($file_path)
+    #for $input_file in $voc_config.collection
+        ln -s '$input_file' 'voc/$input_file.element_identifier' &&
     #end for
 #else
-    DB_PATH="\$(dirname "\$(dirname "\$(which cooc-mutbamscan)")")/share/cojac" &&
-    ln -s "\$DB_PATH" db &&
-    #set $vocdir = 'db/voc'
+    DB_PATH="\$(dirname "\$(dirname "\$(which cojac)")")/share/cojac/voc" &&
+    ln -s "\$DB_PATH" voc &&
 #end if
 ]]></token>
     <token name="@HELP_HEADER@"><![CDATA[
@@ -59,4 +53,4 @@
             <citation type="doi">10.1101/2021.01.08.21249379</citation>
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>