diff jbrowse2.xml @ 34:2893ef33fba9 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd

--- a/jbrowse2.xml	Sat Feb 24 10:44:01 2024 +0000
+++ b/jbrowse2.xml	Sun Feb 25 04:18:53 2024 +0000
@@ -1,4 +1,4 @@
- <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_4" profile="22.05">
+ <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_5" profile="22.05">
     <description>genome browser</description>
     <macros>
         <import>macros.xml</import>
@@ -18,8 +18,7 @@
 --outdir '$output.files_path'
 --xml '$trackxml' &&
 #if $jbgen.zipOut == "true":
-    (cd '$output.files_path' && zip -r - . ) > JBrowse2.zip &&
-    mv JBrowse2.zip '$output'
+    (cd '$output.files_path' && zip -r - . ) > '$output'
 #else
   cp '$output.files_path/index.html' '$output'
 #end if
@@ -471,7 +470,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
+                        <param name="annotation" value="bed/test-3.bed"/>
                     </conditional>
                 </repeat>
             </repeat>
@@ -496,7 +495,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
+                        <param name="annotation" value="gff3/A.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -539,7 +538,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.gff"/>
+                        <param name="annotation" value="gff3/C.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -563,7 +562,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.gff"/>
+                        <param name="annotation" value="gff3/B.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -588,7 +587,7 @@
                 <repeat name="data_tracks">
                     <conditional name="data_format">
                         <param name="data_format_select" value="gene_calls"/>
-                        <param name="annotation" value="gff3/1.gff"/>
+                        <param name="annotation" value="gff3/A.gff"/>
                         <conditional name="match_part">
                             <param name="match_part_select" value="false"/>
                         </conditional>
@@ -686,7 +685,7 @@
                         <has_text text="A.gff"/>
                         <has_text text="B.gff"/>
                         <has_text text="C.gff"/>
-                        <has_text text="D.gff"/>
+                        <has_text text="interpro.gff"/>
                         <has_text text="Scaled Colour"/>
                         <has_text text="1.gff"/>
                         <has_text text="2.gff"/>