Mercurial > repos > devteam > samtools_mpileup

diff samtools_mpileup.xml @ 15:32f6fffbc3e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 13:00:51 +0000
parents b61f5d6a7f25
children 7df230bec125
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line diff
--- a/samtools_mpileup.xml	Mon Nov 20 22:16:18 2023 +0000
+++ b/samtools_mpileup.xml	Thu Jun 19 13:00:51 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.7" profile="@PROFILE@">
+<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.8" profile="@PROFILE@">
     <description>multi-way pileup of variants</description>
     <macros>
         <import>macros.xml</import>
@@ -187,7 +187,7 @@
                     <param name="limit_by_regions" value="limit"/>
                     <param name="region_paste" value="17:1050-1060" />
                 </conditional>
-                <param name="disable_probabilistic_realignment" value="-B" />
+                <param name="disable_probabilistic_realignment" value="true" />
             </conditional>
             <output name="output_file_pu" file="mpileup.out.3" ftype="pileup" />
         </test>
@@ -221,7 +221,7 @@
             </conditional>
             <conditional name="advanced_options">
                 <param name="advanced_options_selector" value="advanced" />
-                <param name="skip_anomalous_read_pairs" value="-A" />
+                <param name="skip_anomalous_read_pairs" value="true" />
             </conditional>
             <output name="output_file_pu" file="samtools_mpileup_out_2.pileup" ftype="pileup" />
         </test>
@@ -268,7 +268,7 @@
 
 **BAQ (Base Alignment Quality)**
 
-BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8 <https://doi.org/10.1093/bioinformatics/btr076>
+BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8
 
 BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option.