# HG changeset patch
# User iuc
# Date 1558981435 14400
# Node ID 4e1d23e5c691466b5fe87a4a64a23231a395196f
# Parent  cf06b44624c785c9d29f7f31689da1800d696c64
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a

diff -r cf06b44624c7 -r 4e1d23e5c691 bcftools_mpileup.xml
--- a/bcftools_mpileup.xml	Thu Feb 21 16:09:57 2019 -0500
+++ b/bcftools_mpileup.xml	Mon May 27 14:23:55 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
     <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
@@ -246,11 +246,12 @@
                     <option value="adjust">Set base and mapping quality options</option>
                 </param>
                 <when value="adjust">
-                    <param name="baq" type="select" optional="true" label="per-Base Alignment Quality">
+                    <param name="baq" type="select" label="per-Base Alignment Quality">
                         <help>
 --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
 --redo-BAQ; ignore existing BQ tags
                         </help>
+                        <option value="">Default</option>
                         <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option>
                         <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option>
                     </param>
@@ -344,6 +345,22 @@
         </test>
         <test>
             <param name="input_number" value="single" />
+            <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
+            <param name="quality_settings" value="adjust" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="mpileup" />
+                    <has_text text="HG00100" />
+                    <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" />
+                    <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_number" value="single" />
             <param name="input_bam" ftype="cram" value="mpileup.3.cram" />
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />