From fa2b6baef71984c0559c53ff5750d1fe9b77163e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 22 Jun 2018 13:22:51 -0400
Subject: [PATCH] Revert "Remove bam to bai converter"

This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb.
---
 config/datatypes_conf.xml.sample               |  1 +
 lib/galaxy/datatypes/converters/bam_to_bai.xml | 14 ++++++++++++++
 2 files changed, 15 insertions(+)
 create mode 100644 lib/galaxy/datatypes/converters/bam_to_bai.xml

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 9fea0cc01d9..10b791f9933 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -9,6 +9,7 @@
     <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
+      <converter file="bam_to_bai.xml" target_datatype="bai"/>
       <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
       <converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
       <display file="ucsc/bam.xml" />
diff --git a/lib/galaxy/datatypes/converters/bam_to_bai.xml b/lib/galaxy/datatypes/converters/bam_to_bai.xml
new file mode 100644
index 00000000000..1587ff83cab
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" version="1.0.0" hidden="true">
+    <requirements>
+        <requirement type="package">samtools</requirement>
+    </requirements>
+    <command>samtools index '$input1' '$output1'</command>
+    <inputs>
+        <param format="bam" name="input1" type="data" label="Choose BAM"/>
+    </inputs>
+    <outputs>
+        <data format="bai" name="output1"/>
+    </outputs>
+    <help>
+    </help>
+</tool>