# HG changeset patch
# User mvdbeek
# Date 1564411940 14400
# Node ID 4237e68132039cf06da19d60c6d03b345bcfe2f0
# Parent  962b7fa09d015ba6661a988b73e9921bb2536fca
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8186814619b9163944e3c11cb797f02c94804ecb

diff -r 962b7fa09d01 -r 4237e6813203 add_matesequence.xml
--- a/add_matesequence.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/add_matesequence.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.3">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.4">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 962b7fa09d01 -r 4237e6813203 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/allow_dovetailing.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.3">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.4">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 962b7fa09d01 -r 4237e6813203 bam_readtagger.xml
--- a/bam_readtagger.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/bam_readtagger.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.3">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.4">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 962b7fa09d01 -r 4237e6813203 extract_variants.xml
--- a/extract_variants.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/extract_variants.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.3">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.4">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 962b7fa09d01 -r 4237e6813203 filter_insertions.xml
--- a/filter_insertions.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/filter_insertions.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.3">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.4">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 962b7fa09d01 -r 4237e6813203 findcluster.xml
--- a/findcluster.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/findcluster.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.3">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.4">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 962b7fa09d01 -r 4237e6813203 plot_coverage.xml
--- a/plot_coverage.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/plot_coverage.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.3">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.4">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 962b7fa09d01 -r 4237e6813203 update_mapq.xml
--- a/update_mapq.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/update_mapq.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.3">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.4">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 962b7fa09d01 -r 4237e6813203 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sun Jul 28 15:58:46 2019 -0400
+++ b/write_supplementary_fastq.xml	Mon Jul 29 10:52:20 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.3">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.4">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.3">readtagger</requirement>
+        <requirement type="package" version="0.5.4">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[