# HG changeset patch
# User mvdbeek
# Date 1576679271 18000
# Node ID b090e190c813255766de650af998ae12c97d449e
# Parent f383ca1c50336cdbf09a5150d5a0165fece5bf26
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 11ea16568d776a1dd68bb1ead50695ea8769f201"
diff -r f383ca1c5033 -r b090e190c813 add_matesequence.xml
--- a/add_matesequence.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/add_matesequence.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.17">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.18">
<description>into tag field</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>add_matesequence --version</version_command>
<command detect_errors="aggressive"><![CDATA[
diff -r f383ca1c5033 -r b090e190c813 allow_dovetailing.xml
--- a/allow_dovetailing.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/allow_dovetailing.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.17">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.18">
<description>modifies proper_pair flag in bam files</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<command detect_errors="aggressive"><![CDATA[
allow_dovetailing -i '$input' -o '$output'
diff -r f383ca1c5033 -r b090e190c813 bam_readtagger.xml
--- a/bam_readtagger.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/bam_readtagger.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.17">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.18">
<description>from multiple bam files</description>
<macros>
<import>macros.xml</import>
</macros>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<command detect_errors="aggressive"><![CDATA[
readtagger -t '$tag_file' -s
diff -r f383ca1c5033 -r b090e190c813 extract_variants.xml
--- a/extract_variants.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/extract_variants.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.17">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.18">
<description>from long reads</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>extract_variants --version</version_command>
<command detect_errors="aggressive"><![CDATA[
diff -r f383ca1c5033 -r b090e190c813 filter_insertions.xml
--- a/filter_insertions.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/filter_insertions.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.17">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.18">
<description>based on softclips in control files</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>confirm_insertions --version</version_command>
<command detect_errors="aggressive"><![CDATA[
diff -r f383ca1c5033 -r b090e190c813 findcluster.xml
--- a/findcluster.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/findcluster.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.17">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.18">
<description>in bam files</description>
<macros>
<import>macros.xml</import>
</macros>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>findcluster --version</version_command>
<command detect_errors="aggressive"><![CDATA[
diff -r f383ca1c5033 -r b090e190c813 normalize_readsizes.xml
--- a/normalize_readsizes.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/normalize_readsizes.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.17">
+<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.18">
<description>of multiple fastq files</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>normalize_readsizes --version</version_command>
<command detect_errors="aggressive"><![CDATA[
diff -r f383ca1c5033 -r b090e190c813 plot_coverage.xml
--- a/plot_coverage.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/plot_coverage.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.17">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.18">
<description>as area plot between BAM files</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<command detect_errors="aggressive"><![CDATA[
#import re
diff -r f383ca1c5033 -r b090e190c813 update_mapq.xml
--- a/update_mapq.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/update_mapq.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.17">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.18">
<description>of supplementary alignments</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>update_mapq --version</version_command>
<command detect_errors="aggressive"><![CDATA[
diff -r f383ca1c5033 -r b090e190c813 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml Tue Nov 05 05:06:18 2019 -0500
+++ b/write_supplementary_fastq.xml Wed Dec 18 09:27:51 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.17">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.18">
<description>from SAM/BAM alignment files as FASTQ</description>
<requirements>
- <requirement type="package" version="0.5.17">readtagger</requirement>
+ <requirement type="package" version="0.5.18">readtagger</requirement>
</requirements>
<version_command>write_supplementary_fastq --version</version_command>
<command detect_errors="aggressive"><![CDATA[