Mercurial > repos > iuc > gemini_load

diff gemini_load.xml @ 5:b382ddaf8445 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 12:36:51 -0500
parents 264f4601dd1d
children 424f44e3448d
line wrap: on
line diff
--- a/gemini_load.xml	Fri Dec 07 12:51:01 2018 -0500
+++ b/gemini_load.xml	Fri Dec 14 12:36:51 2018 -0500
@@ -81,12 +81,45 @@
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="gemini_load_input.vcf" ftype="vcf" />
+            <param name="annotation_databases" value="1999-01-01" />
+            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
+            <param name="skip_gene_tables" value="False" />
+            <param name="skip_gerp_bp" value="True" />
+            <param name="skip_cadd" value="True" />
+            <param name="no_genotypes" value="False" />
+            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+        </test>
+        <test>
+            <param name="annotation_databases" value="1999-01-01" />
+            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
+            <param name="skip_gene_tables" value="False" />
+            <param name="skip_gerp_bp" value="False" />
+            <param name="skip_cadd" value="False" />
+            <param name="no_genotypes" value="False" />
+            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <assert_stderr>
+                <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
+                <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
+            </assert_stderr>
+        </test>
+        <test>
+            <param name="annotation_databases" value="1999-01-01" />
+            <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="skip_gene_tables" value="True" />
             <param name="skip_gerp_bp" value="True" />
             <param name="skip_cadd" value="True" />
             <param name="no_genotypes" value="True" />
-            <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/>
+            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+        </test>
+        <test>
+            <param name="annotation_databases" value="1999-01-01" />
+            <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
+            <param name="skip_gene_tables" value="False" />
+            <param name="skip_gerp_bp" value="True" />
+            <param name="skip_cadd" value="True" />
+            <param name="no_genotypes" value="False" />
+            <param name="ped" value="gemini_amend.ped" ftype="tabular" />
+            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
         </test>
     </tests>
     <help><![CDATA[