# HG changeset patch
# User iuc
# Date 1579905320 18000
# Node ID 567837ca5f332c22ed4b3088af4823c2ee92a5b9
# Parent  0c8f7322f8fc5b0553865ad5aeee52e6ff1f34ad
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"

diff -r 0c8f7322f8fc -r 567837ca5f33 gemini_annotate.xml
--- a/gemini_annotate.xml	Fri Jan 18 19:34:41 2019 -0500
+++ b/gemini_annotate.xml	Fri Jan 24 17:35:20 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>the variants in an existing GEMINI database with additional information</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -19,9 +19,19 @@
 <![CDATA[
 
     ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz
-    #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
-    bgzip -c '$annotate_source' > '$tabixed_file' &&
-    tabix -p '$annotate_source.ext' '$tabixed_file' &&
+    #if $annotate_source.ext == 'vcf_bgzip':
+        ## File is bgzipped and tabixed already -> just symlink data and index
+        #set $tabixed_file = 'tabixed.vcf.gz'
+        ln -s '$annotate_source' $tabixed_file &&
+        ln -s '$annotate_source.metadata.tabix_index' ${tabixed_file}.tbi &&
+    #else:
+        ## bgzip and index vcf or bed
+        #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext
+        bgzip -c '$annotate_source' > '$tabixed_file' &&
+        tabix -p '$annotate_source.ext' '$tabixed_file' &&
+    #end if
+    ## gemini annotate modifies its input database in-place so, in Galaxy,
+    ## we need to create a copy first!
     cp '$infile' '$outfile' &&
 
     gemini @BINARY@
@@ -46,7 +56,7 @@
         #else:
             -c '${a.column_name}'
         #end if
-        #if str($annotate_source.ext) == "vcf":
+        #if str($annotate_source.ext) != "bed":
             $region_only
         #end if
         '$outfile'
@@ -54,7 +64,7 @@
     </command>
     <inputs>
         <expand macro="infile" />
-        <param argument="-f" name="annotate_source" type="data" format="vcf,bed"
+        <param argument="-f" name="annotate_source" type="data" format="vcf,vcf_bgzip,bed"
         label="Dataset to use as the annotation source"
         help="The tool can use the information from a BED or VCF dataset to annotate the database variants."/>
         <param argument="--region-only" name="region_only" type="boolean" checked="true" truevalue="" falsevalue="--region-only"
@@ -112,19 +122,43 @@
     </outputs>
     <tests>
         <test>
+            <!-- test with annotation source in bed format -->
             <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
-            <param name="annotate_source" value="anno.bed" />
+            <param name="annotate_source" value="anno.bed" ftype="bed" />
             <param name="region_only" value="false" />
             <conditional name="a">
                 <param name="a_selector" value="count" />
                 <param name="column_name" value="anno5" />
             </conditional>
             <assert_command>
+                <!-- confirm region_only gets ignored for bed input -->
                 <not_has_text text="--region-only" />
             </assert_command>
             <output name="outfile" file="gemini_annotate_result.db" ftype="gemini.sqlite" compare="sim_size" delta="1000"/>
         </test>
         <test>
+            <!-- test with annotation source in vcf format -->
+            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
+            <param name="annotate_source" value="gemini_amend.vcf" ftype="vcf" />
+            <param name="region_only" value="false" />
+            <conditional name="a">
+                <param name="a_selector" value="count" />
+                <param name="column_name" value="anno5" />
+            </conditional>
+            <output name="outfile" file="gemini_annotate_result.db" ftype="gemini.sqlite" compare="sim_size" delta="1000"/>
+        </test>
+        <test>
+            <!-- test with annotation source in vcf_bgzip format -->
+            <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
+            <param name="annotate_source" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" />
+            <param name="region_only" value="false" />
+            <conditional name="a">
+                <param name="a_selector" value="count" />
+                <param name="column_name" value="anno5" />
+            </conditional>
+            <output name="outfile" file="gemini_annotate_result.db" ftype="gemini.sqlite" compare="sim_size" delta="1000"/>
+        </test>
+        <test>
             <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
             <param name="annotate_source" value="anno.bed" />
             <conditional name="a">
@@ -138,8 +172,8 @@
             </conditional>
             <assert_command>
                 <has_text_matching expression="-a +extract" />
-                <has_text_matching expression="-e +1" />
-                <has_text_matching expression="-c +anno5" />
+                <has_text_matching expression="-e +&apos;1&apos;" />
+                <has_text_matching expression="-c +&apos;anno5&apos;" />
                 <has_text_matching expression="-t +text" />
                 <has_text_matching expression="-o +first" />
             </assert_command>
@@ -164,8 +198,8 @@
             </conditional>
             <assert_command>
                 <has_text_matching expression="-a +extract" />
-                <has_text_matching expression="-e +1,2" />
-                <has_text_matching expression="-c +anno5,anno6" />
+                <has_text_matching expression="-e +&apos;1,2&apos;" />
+                <has_text_matching expression="-c +&apos;anno5,anno6&apos;" />
                 <has_text_matching expression="-t +text,integer" />
                 <has_text_matching expression="-o +first,first" />
             </assert_command>
diff -r 0c8f7322f8fc -r 567837ca5f33 test-data/gemini_amend.vcf.gz
Binary file test-data/gemini_amend.vcf.gz has changed