diff gemini_load.xml @ 7:64132aa2d62a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"

--- a/gemini_load.xml	Wed Feb 06 10:58:17 2019 -0500
+++ b/gemini_load.xml	Fri Jan 24 17:33:33 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy1">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
     <description>Loading a VCF file into GEMINI</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -11,9 +11,15 @@
 <![CDATA[
         @PROVIDE_ANNO_DATA@
 
-        ln -s '$infile' input.vcf &&
-        bgzip -c input.vcf > input.vcf.gz &&
-        tabix -p vcf input.vcf.gz &&
+        ## gemini load expects a bgzipped and tabixed vcf as input
+        #set $tabixed_file = 'input.vcf.gz'
+        #if $infile.ext == 'vcf':
+            bgzip -c '$infile' > $tabixed_file &&
+            tabix -p vcf $tabixed_file &&
+        #else:
+            ln -s '$infile' $tabixed_file &&
+            ln -s '$infile.metadata.tabix_index' ${tabixed_file}.tbi &&
+        #end if
 
         gemini
             @BINARY@
@@ -56,7 +62,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="vcf"
+        <param name="infile" type="data" format="vcf,vcf_bgzip"
         label="VCF dataset to be loaded in the GEMINI database"
         help="Only build 37 (aka hg19) of the human genome is supported.">
             <options>
@@ -157,6 +163,14 @@
             <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>
+        <test>
+            <param name="annotation_databases" value="1999-01-01" />
+            <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" />
+            <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
+            <param name="has_genotypes" value="True" />
+            <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[
 .. class:: Warning mark