# HG changeset patch
# User iuc
# Date 1642253422 0
# Node ID 6d7dc9a1bef3c3dc36612b2dc195c158c819c8d6
# Parent  ce9396ddcb2b6b05f08d8d299c298f81a930c493
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"

diff -r ce9396ddcb2b -r 6d7dc9a1bef3 bcftools_mpileup.xml
--- a/bcftools_mpileup.xml	Thu Oct 14 10:16:46 2021 +0000
+++ b/bcftools_mpileup.xml	Sat Jan 15 13:30:22 2022 +0000
@@ -1,7 +1,6 @@
 <?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>
-    <expand macro="bio_tools" />
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
         <import>macros.xml</import>
@@ -19,6 +18,7 @@
             <option value="1024">The read is a PCR or optical duplicate</option>
         </xml>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements">
         <expand macro="samtools_requirement"/>
     </expand>
@@ -223,7 +223,7 @@
         </section>
 
         <section name="sec_filtering" expanded="false" title="Input Filtering Options">
-            <param name="max_reads_per_bam" type="integer" value="250" max="1024" min="1" label="Max reads per BAM" help="--max-depth; default=250"/>
+            <param name="max_reads_per_bam" type="integer" value="250" min="1" label="Max reads per BAM" help="--max-depth; default=250"/>
             <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/>
             <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/>
             <conditional name="filter_by_flags">