# HG changeset patch
# User mvdbeek
# Date 1490535873 14400
# Node ID da147eb69dd266a102b360fbe991b9509132d085
# Parent  eaca702e7f3b3363b53d88405f4dce46956e3413
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8fd2a671b42153cbc4809577c808d56d959881f4

diff -r eaca702e7f3b -r da147eb69dd2 add_matesequence.xml
--- a/add_matesequence.xml	Fri Mar 24 12:26:47 2017 -0400
+++ b/add_matesequence.xml	Sun Mar 26 09:44:33 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.8">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.9">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.8">readtagger</requirement>
+        <requirement type="package" version="0.3.9">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r eaca702e7f3b -r da147eb69dd2 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Fri Mar 24 12:26:47 2017 -0400
+++ b/allow_dovetailing.xml	Sun Mar 26 09:44:33 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.8">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.9">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.8">readtagger</requirement>
+        <requirement type="package" version="0.3.9">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r eaca702e7f3b -r da147eb69dd2 bam_readtagger.xml
--- a/bam_readtagger.xml	Fri Mar 24 12:26:47 2017 -0400
+++ b/bam_readtagger.xml	Sun Mar 26 09:44:33 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.8">
-    <description>from multiple sam/bam files123</description>
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.9">
+    <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.8">readtagger</requirement>
+        <requirement type="package" version="0.3.9">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
diff -r eaca702e7f3b -r da147eb69dd2 deploy.sh
diff -r eaca702e7f3b -r da147eb69dd2 findcluster.xml
--- a/findcluster.xml	Fri Mar 24 12:26:47 2017 -0400
+++ b/findcluster.xml	Sun Mar 26 09:44:33 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.8">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.9">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.8">readtagger</requirement>
+        <requirement type="package" version="0.3.9">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r eaca702e7f3b -r da147eb69dd2 test-data/extended_and_annotated_roi.bam.bai
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
diff -r eaca702e7f3b -r da147eb69dd2 test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Fri Mar 24 12:26:47 2017 -0400
+++ b/test-data/three_cluster_out.gff	Sun Mar 26 09:44:33 2017 -0400
@@ -1,4 +1,4 @@
 ##gff-version 3
-3R	findcluster	TE	13373515	13373524	27	+	.	ID=extended_and_annotated_roi.bam_0;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=14;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False
-3R	findcluster	TE	13374595	13374595	2	+	.	ID=extended_and_annotated_roi.bam_1;left_insert=0,GTTCACCCGCGTCCGAGTTCCTGCTCCACTACTCCCTGGCTGCTGACTCACTGTTGTTATAGGGGTGGCTTCCCCTCTGTTCTTCCTGGGGGAATGCTGCATCTTCCCCAGCTCCAAAATGGCGG;left_support=2;right_insert=;right_support=0;valid_TSD=False
-3R	findcluster	TE	13374677	13374677	1	+	.	ID=extended_and_annotated_roi.bam_2;left_insert=;left_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=0.0,9.53673406912e-07,0.999999046327;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=14;non_support=;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=;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=;right_insert=;right_support=1;valid_TSD=False
diff -r eaca702e7f3b -r da147eb69dd2 update_mapq.xml
--- a/update_mapq.xml	Fri Mar 24 12:26:47 2017 -0400
+++ b/update_mapq.xml	Sun Mar 26 09:44:33 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.8">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.9">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.8">readtagger</requirement>
+        <requirement type="package" version="0.3.9">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r eaca702e7f3b -r da147eb69dd2 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Fri Mar 24 12:26:47 2017 -0400
+++ b/write_supplementary_fastq.xml	Sun Mar 26 09:44:33 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.8">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.9">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.8">readtagger</requirement>
+        <requirement type="package" version="0.3.9">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[