# HG changeset patch
# User mvdbeek
# Date 1492977533 14400
# Node ID 42fefb316c95ac2197c4acb1512de37c208e72cd
# Parent  1c91108a80d5512a6de6c7d009008306273b80e2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 16f35b0e373f4cbd33f1bc6aef4a13b7fd2eca12-dirty

diff -r 1c91108a80d5 -r 42fefb316c95 add_matesequence.xml
--- a/add_matesequence.xml	Thu Apr 20 11:04:08 2017 -0400
+++ b/add_matesequence.xml	Sun Apr 23 15:58:53 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.15">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.16">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.15">readtagger</requirement>
+        <requirement type="package" version="0.3.16">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 1c91108a80d5 -r 42fefb316c95 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Thu Apr 20 11:04:08 2017 -0400
+++ b/allow_dovetailing.xml	Sun Apr 23 15:58:53 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.15">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.16">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.15">readtagger</requirement>
+        <requirement type="package" version="0.3.16">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 1c91108a80d5 -r 42fefb316c95 bam_readtagger.xml
--- a/bam_readtagger.xml	Thu Apr 20 11:04:08 2017 -0400
+++ b/bam_readtagger.xml	Sun Apr 23 15:58:53 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.15">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.16">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.15">readtagger</requirement>
+        <requirement type="package" version="0.3.16">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
@@ -16,6 +16,7 @@
         $discarded
         $verified
         $discard_proper_pairs
+        --cores "\${GALAXY_SLOTS:-2}"
         -o '$tagged_file'
     ]]></command>
     <inputs>
diff -r 1c91108a80d5 -r 42fefb316c95 findcluster.xml
--- a/findcluster.xml	Thu Apr 20 11:04:08 2017 -0400
+++ b/findcluster.xml	Sun Apr 23 15:58:53 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.15">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.16">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.15">readtagger</requirement>
+        <requirement type="package" version="0.3.16">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/a_pasteurianus_tagged_with_dm6.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/a_pasteurianus_tagged_with_dm6_discarded.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6_discarded.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/a_pasteurianus_tagged_with_dm6_verified.bam
Binary file test-data/a_pasteurianus_tagged_with_dm6_verified.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/dm6_tagged_with_a_pasteurianus.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/dm6_tagged_with_a_pasteurianus_discarded.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus_discarded.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/dm6_tagged_with_a_pasteurianus_verified.bam
Binary file test-data/dm6_tagged_with_a_pasteurianus_verified.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/proper_pair_discard_out.bam
Binary file test-data/proper_pair_discard_out.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/proper_pair_discard_verified_empty.bam
Binary file test-data/proper_pair_discard_verified_empty.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 test-data/proper_pair_out_suboptimal_tags.bam
Binary file test-data/proper_pair_out_suboptimal_tags.bam has changed
diff -r 1c91108a80d5 -r 42fefb316c95 update_mapq.xml
--- a/update_mapq.xml	Thu Apr 20 11:04:08 2017 -0400
+++ b/update_mapq.xml	Sun Apr 23 15:58:53 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.15">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.16">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.15">readtagger</requirement>
+        <requirement type="package" version="0.3.16">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 1c91108a80d5 -r 42fefb316c95 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Thu Apr 20 11:04:08 2017 -0400
+++ b/write_supplementary_fastq.xml	Sun Apr 23 15:58:53 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.15">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.16">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.15">readtagger</requirement>
+        <requirement type="package" version="0.3.16">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[