# HG changeset patch
# User mvdbeek
# Date 1490992087 14400
# Node ID 8d201345f6dcbfd9dfd9a1597bf4bb13fe6d8bbc
# Parent  4a14e25b9ea15d4dabb005163d298e0680f1541c
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c12b0c1b22f03c95651e19f32a2065a79a57188a

diff -r 4a14e25b9ea1 -r 8d201345f6dc add_matesequence.xml
--- a/add_matesequence.xml	Tue Mar 28 09:33:11 2017 -0400
+++ b/add_matesequence.xml	Fri Mar 31 16:28:07 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.11">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.12">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.11">readtagger</requirement>
+        <requirement type="package" version="0.3.12">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 4a14e25b9ea1 -r 8d201345f6dc allow_dovetailing.xml
--- a/allow_dovetailing.xml	Tue Mar 28 09:33:11 2017 -0400
+++ b/allow_dovetailing.xml	Fri Mar 31 16:28:07 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.11">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.12">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.11">readtagger</requirement>
+        <requirement type="package" version="0.3.12">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 4a14e25b9ea1 -r 8d201345f6dc bam_readtagger.xml
--- a/bam_readtagger.xml	Tue Mar 28 09:33:11 2017 -0400
+++ b/bam_readtagger.xml	Fri Mar 31 16:28:07 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.11">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.12">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.11">readtagger</requirement>
+        <requirement type="package" version="0.3.12">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
diff -r 4a14e25b9ea1 -r 8d201345f6dc findcluster.xml
--- a/findcluster.xml	Tue Mar 28 09:33:11 2017 -0400
+++ b/findcluster.xml	Fri Mar 31 16:28:07 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.11">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.12">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.11">readtagger</requirement>
+        <requirement type="package" version="0.3.12">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 4a14e25b9ea1 -r 8d201345f6dc test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Tue Mar 28 09:33:11 2017 -0400
+++ b/test-data/three_cluster_out.gff	Fri Mar 31 16:28:07 2017 -0400
@@ -1,4 +1,4 @@
 ##gff-version 3
-3R	findcluster	TE	13373515	13373524	27	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=0.0,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=14;non_support=0;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False
-3R	findcluster	TE	13374595	13374595	2	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=0.0,0.333333333333,0.666666666667;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;non_support=0;right_insert=;right_support=0;valid_TSD=False
-3R	findcluster	TE	13374677	13374677	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=heterozygous;genotype_likelihoods=0.0,0.5;left_insert=;left_support=0;non_support=0;right_insert=;right_support=1;valid_TSD=False
+3R	findcluster	TE	13373515	13373524	27	+	.	ID=extended_and_annotated_roi.bam_0;genotype=homozygous;genotype_likelihoods=1.8828617809e-31,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=14;non_support=0;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False
+3R	findcluster	TE	13374595	13374595	2	+	.	ID=extended_and_annotated_roi.bam_1;genotype=homozygous;genotype_likelihoods=0.0106846062525,0.329771797916,0.659543595832;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;non_support=0;right_insert=;right_support=0;valid_TSD=False
+3R	findcluster	TE	13374677	13374677	1	+	.	ID=extended_and_annotated_roi.bam_2;genotype=heterozygous;genotype_likelihoods=0.212598425197,0.393700787402;left_insert=;left_support=0;non_support=0;right_insert=;right_support=1;valid_TSD=False
diff -r 4a14e25b9ea1 -r 8d201345f6dc update_mapq.xml
--- a/update_mapq.xml	Tue Mar 28 09:33:11 2017 -0400
+++ b/update_mapq.xml	Fri Mar 31 16:28:07 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.11">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.12">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.11">readtagger</requirement>
+        <requirement type="package" version="0.3.12">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 4a14e25b9ea1 -r 8d201345f6dc write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Tue Mar 28 09:33:11 2017 -0400
+++ b/write_supplementary_fastq.xml	Fri Mar 31 16:28:07 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.11">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.12">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.11">readtagger</requirement>
+        <requirement type="package" version="0.3.12">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[