Mercurial > repos > iuc > gemini_stats

diff gemini_stats.xml @ 5:78e971dd87ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:28:45 -0500
parents ed118e624798
children c60ef99f03d3
line wrap: on
line diff
--- a/gemini_stats.xml	Sat Dec 08 10:23:30 2018 -0500
+++ b/gemini_stats.xml	Fri Dec 14 12:28:45 2018 -0500
@@ -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[