diff gemini_pathways.xml @ 4:69b5327a1f88 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

--- a/gemini_pathways.xml	Wed Oct 17 13:26:31 2018 -0400
+++ b/gemini_pathways.xml	Fri Dec 14 13:02:36 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
     <description>Map genes and variants to KEGG pathways</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -9,10 +9,9 @@
     <expand macro="version_command" />
     <command>
 <![CDATA[
+        @PROVIDE_ANNO_DATA@
+
         gemini
-            #if $annotation_databases:
-                --annotation-dir "${annotation_databases.fields.path}"
-            #end if
             @BINARY@
             -v $ensembl
             $lof
@@ -37,9 +36,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
+            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
             <param name="ensembl" value="68" />
-            <output name="outfile" file="gemini_pathways_result.tabular" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>