From 9d98f10767d7c43e979720ba8a9badee86501c78 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 6 Jul 2017 20:23:10 +0200
Subject: [PATCH] Adding test tool

---
 lib/galaxy/datatypes/tabular.py             |  4 +--
 test/functional/tools/samples_tool_conf.xml |  1 +
 test/functional/tools/vcf_bgzip.xml         | 30 +++++++++++++++++++++
 3 files changed, 33 insertions(+), 2 deletions(-)
 create mode 100644 test/functional/tools/vcf_bgzip.xml

diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 0736d4f7429..11ac1d079e4 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -741,7 +741,7 @@ class VcfGz( BaseVcf, binary.Binary):
     extension = 'vcf.gz'
     compressed = True
 
-    MetadataElement( name="vcf_gz_index", desc="Vcf Index File", param=metadata.FileParameter, file_ext="tbi", readonly=True, no_value=None, visible=False, optional=True )
+    MetadataElement( name="tabix_index", desc="Vcf Index File", param=metadata.FileParameter, file_ext="tbi", readonly=True, no_value=None, visible=False, optional=True )
 
     def set_meta( self, dataset, **kwd ):
         super(BaseVcf, self).set_meta(dataset, **kwd)
@@ -749,7 +749,7 @@ class VcfGz( BaseVcf, binary.Binary):
         # These metadata values are not accessible by users, always overwrite
         index_file = dataset.metadata.bcf_index
         if not index_file:
-            index_file = dataset.metadata.spec['vcf_gz_index'].param.new_file( dataset=dataset )
+            index_file = dataset.metadata.spec['tabix_index'].param.new_file( dataset=dataset )
         # Create the bcf index
         # $ bcftools index
         # Usage: bcftools index <in.bcf>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 4197eb61b5f..839b888bb92 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -25,6 +25,7 @@
   <tool file="composite_output.xml" />
   <tool file="composite_output_tests.xml" />
   <tool file="unicode_stream.xml" />
+  <tool file="vcf_bgzip.xml" />
   <tool file="metadata.xml" />
   <tool file="metadata_bam.xml" />
   <tool file="metadata_bcf.xml" />
diff --git a/test/functional/tools/vcf_bgzip.xml b/test/functional/tools/vcf_bgzip.xml
new file mode 100644
index 00000000000..a72077c089b
--- /dev/null
+++ b/test/functional/tools/vcf_bgzip.xml
@@ -0,0 +1,30 @@
+<tool id="vcf_bgzip_test" name="vcf_bgzip_test" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.4">bcftools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      ln -s $input input.vcf.gz &&
+      tabix -p vcf input.vcf.gz &&
+      md5sum input.vcf.gz.tbi > input.vcf.gz.tbi.md5 &&
+      cp $input.metadata.vcf_gz_index input.vcf.gz.tbi &&
+      md5check -c vcf.gz.tbi.md5 &&
+      cp $input $output
+    ]]></command>
+    <inputs>
+        <param name="input" format="vcf_bgzip" type="data" label="Source file"/>
+    </inputs>
+    <outputs>
+        <data format="data" ftype="vcf_bgzip" name="output" />
+    </outputs>
+  <tests>
+    <test>
+      <param name="input" ftype="vcf_bgzip" value="test.vcf.gz"/>
+      <output name="output" file="test.vcf.gz"/>
+    </test>
+  </tests>
+    <help><![CDATA[
+        This is a help text
+    ]]></help>
+    <citations>
+    </citations>
+</tool>