diff gemini_interactions.xml @ 4:a6d326ffbb72 draft

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

--- a/gemini_interactions.xml	Wed Oct 17 13:33:09 2018 -0400
+++ b/gemini_interactions.xml	Fri Dec 14 12:50:32 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>Find genes among variants that are interacting partners</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -9,11 +9,9 @@
     <expand macro="version_command" />
     <command>
 <![CDATA[
+        @PROVIDE_ANNO_DATA@
+
         gemini
-            #if $annotation_databases:
-                --annotation-dir "${annotation_databases.fields.path}"
-            #end if
-
             #if $gene.gene_selector == 'lof':
                 ## lof interactions is a separate program
                 lof_interactions
@@ -51,10 +49,14 @@
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
-            <param name="gene" value="CTBP2" />
+            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
+            <param name="gene" value="BCL6" />
             <param name="radius" value="5" />
-            <output name="outfile" file="gemini_interactions_result.tabular" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="sample&#009;gene&#009;order_of_interaction&#009;interacting_gene.*" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[