# HG changeset patch
# User mvdbeek
# Date 1486749643 18000
# Node ID d05f883765ba320e3fd860c5195e704a04b22268
# Parent  8138277ea0e5ba694223acb88db3220bf962743b
planemo upload for repository https://github.com/bardin-lab/tag_reads/tree/master/galaxy commit deb166021688193b84e799315b08d31518009583

diff -r 8138277ea0e5 -r d05f883765ba bam_tag_reads.xml
--- a/bam_tag_reads.xml	Wed Feb 08 03:36:05 2017 -0500
+++ b/bam_tag_reads.xml	Fri Feb 10 13:00:43 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_tag_reads" name="Tag alignment files" version="0.1.3">
+<tool id="bam_tag_reads" name="Tag alignment files" version="0.1.4">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.1.3">tag_reads</requirement>
+        <requirement type="package" version="0.1.4">tag_reads</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         tag_reads -t '$tag_file' -a
@@ -12,6 +12,7 @@
             '$element.annotate_with':$element.r_tag:$element.m_tag
         #end for
         $allow_dovetailing
+        $keep_suboptimal
         -o '$tagged_file'
     ]]></command>
     <inputs>
@@ -26,6 +27,7 @@
             </param>
         </repeat>
         <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
+        <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/>
     </inputs>
     <outputs>
         <data name="tagged_file" format="bam"/>
diff -r 8138277ea0e5 -r d05f883765ba test-data/test.bam
Binary file test-data/test.bam has changed
diff -r 8138277ea0e5 -r d05f883765ba test-data/test.out
Binary file test-data/test.out has changed
diff -r 8138277ea0e5 -r d05f883765ba test-data/test2.bam
Binary file test-data/test2.bam has changed