diff gemini_stats.xml @ 4:cdd90678004a draft

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

--- a/gemini_stats.xml	Wed Oct 17 13:33:53 2018 -0400
+++ b/gemini_stats.xml	Fri Dec 14 12:47:19 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>Compute useful variant statistics</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -45,16 +45,30 @@
         <param name="summarize" type="text" area="True" size="5x50" label="The query to be issued to the database to summarize" help="(--summarize)">
             <expand macro="sanitize_query" />
         </param>
-
     </inputs>
     <outputs>
         <data name="outfile" format="tabular" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
+            <!-- test vars-by-sample report -->
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
             <param name="stats_type" value="--vars-by-sample" />
-            <output name="outfile" file="gemini_stats_result.tabular" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="sample&#009;total" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <!-- test gts-by-sample report -->
+            <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
+            <param name="stats_type" value="--gts-by-sample" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_line_matching expression="sample&#009;num_hom_ref&#009;num_het&#009;num_hom_alt&#009;num_unknown&#009;total" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[