# HG changeset patch
# User mvdbeek
# Date 1564343954 14400
# Node ID b50e114fece90092676afbad4bdc3b13ab4ae2d0
# Parent  5c96f12f837d82c02a24a327158ce6b1563f14e6
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c3a7b2f6aa429ea2881ee8d111ace3cce95bb9e7

diff -r 5c96f12f837d -r b50e114fece9 add_matesequence.xml
--- a/add_matesequence.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/add_matesequence.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.2">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.3">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5c96f12f837d -r b50e114fece9 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/allow_dovetailing.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.2">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.3">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 5c96f12f837d -r b50e114fece9 bam_readtagger.xml
--- a/bam_readtagger.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/bam_readtagger.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.2">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.3">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 5c96f12f837d -r b50e114fece9 extract_variants.xml
--- a/extract_variants.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/extract_variants.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.2">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.3">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5c96f12f837d -r b50e114fece9 filter_insertions.xml
--- a/filter_insertions.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/filter_insertions.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.2">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.3">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5c96f12f837d -r b50e114fece9 findcluster.xml
--- a/findcluster.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/findcluster.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.2">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.3">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5c96f12f837d -r b50e114fece9 plot_coverage.xml
--- a/plot_coverage.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/plot_coverage.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.2">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.3">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 5c96f12f837d -r b50e114fece9 test-data/extended_and_annotated_roi.bam.bai
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
diff -r 5c96f12f837d -r b50e114fece9 test-data/out.png
Binary file test-data/out.png has changed
diff -r 5c96f12f837d -r b50e114fece9 test-data/three_cluster_out.bam.bai
Binary file test-data/three_cluster_out.bam.bai has changed
diff -r 5c96f12f837d -r b50e114fece9 update_mapq.xml
--- a/update_mapq.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/update_mapq.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.2">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.3">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5c96f12f837d -r b50e114fece9 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sun Jul 28 13:50:05 2019 -0400
+++ b/write_supplementary_fastq.xml	Sun Jul 28 15:59:14 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.2">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.3">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.2">readtagger</requirement>
+        <requirement type="package" version="0.5.3">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[