diff gemini_load.xml @ 4:5c5cdbdc3534 draft

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

--- a/gemini_load.xml	Wed Oct 17 13:25:58 2018 -0400
+++ b/gemini_load.xml	Fri Dec 14 13:01:22 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>Loading a VCF file into GEMINI</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -9,14 +9,13 @@
     <expand macro="version_command" />
     <command>
 <![CDATA[
+        @PROVIDE_ANNO_DATA@
+
         ln -s "${ infile }" input.vcf &&
         bgzip -c input.vcf > input.vcf.gz &&
         tabix -p vcf input.vcf.gz &&
 
         gemini
-            #if $annotation_databases:
-                --annotation-dir "${annotation_databases.fields.path}"
-            #end if
             @BINARY@
             -v input.vcf.gz
             #if str( $annotation_type ) != "None":
@@ -82,12 +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[