# HG changeset patch
# User mvdbeek
# Date 1488738582 18000
# Node ID bf8ffb337cbef98969404cc507b38ff4697a3ec0
# Parent  d2009cdcdebaed1de6aa824e28dc932e48a4c150
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8-dirty

diff -r d2009cdcdeba -r bf8ffb337cbe add_matesequence.xml
--- a/add_matesequence.xml	Fri Mar 03 10:30:14 2017 -0500
+++ b/add_matesequence.xml	Sun Mar 05 13:29:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.3">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.4">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.3">readtagger</requirement>
+        <requirement type="package" version="0.3.4">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r d2009cdcdeba -r bf8ffb337cbe allow_dovetailing.xml
--- a/allow_dovetailing.xml	Fri Mar 03 10:30:14 2017 -0500
+++ b/allow_dovetailing.xml	Sun Mar 05 13:29:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.3">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.4">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.3">readtagger</requirement>
+        <requirement type="package" version="0.3.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r d2009cdcdeba -r bf8ffb337cbe bam_readtagger.xml
--- a/bam_readtagger.xml	Fri Mar 03 10:30:14 2017 -0500
+++ b/bam_readtagger.xml	Sun Mar 05 13:29:42 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.3">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.4">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.3">readtagger</requirement>
+        <requirement type="package" version="0.3.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
diff -r d2009cdcdeba -r bf8ffb337cbe findcluster.xml
--- a/findcluster.xml	Fri Mar 03 10:30:14 2017 -0500
+++ b/findcluster.xml	Sun Mar 05 13:29:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.3">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.4">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.3">readtagger</requirement>
+        <requirement type="package" version="0.3.4">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -10,6 +10,7 @@
         --output_bam '$output_bam'
         --output_gff '$output_gff'
         --sample_name '$input.element_identifier'
+        --threads "\${GALAXY_SLOTS:-2}"
     ]]></command>
     <inputs>
         <param name="input" argument="--input_path" type="data" format="bam"/>
diff -r d2009cdcdeba -r bf8ffb337cbe test-data/three_cluster_out.bam
Binary file test-data/three_cluster_out.bam has changed
diff -r d2009cdcdeba -r bf8ffb337cbe test-data/three_cluster_out.gff
--- a/test-data/three_cluster_out.gff	Fri Mar 03 10:30:14 2017 -0500
+++ b/test-data/three_cluster_out.gff	Sun Mar 05 13:29:42 2017 -0500
@@ -1,6 +1,4 @@
 ##gff-version 3
-3R	findcluster	TE	13373515	13373524	39	+	.	ID=extended_and_annotated_roi.bam_0;left_insert=0,CTCGGAATGTATCTAACTAACAAACTCATATCAAATATAAGCAAGTGCGCCAATTCGTATGCATATGGACATATGGACATATACATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATCAAACCAGCTTACATTTTTACTTACACTTAAGCGCATGATTTGTTGTGCATCCATACCGTTATTTTTCC;left_support=26;right_insert=0,CTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCCAAACTAAAAAAATACCTCGTGTTGATTCTGAAACTTCTTTAAAGGCGTTGATCTTAGTCAAACGACGGATCATTTGTTCGACTCGAATAGTAAAATACGTAAGTATATAGATAGTCTATATTAATTTTAAAAGCTCAAAGGGGCGCAAGTCTCTCTCATCAGTTGTGTCTTTAGTTTTTTTGATTTGGTTTGGTG;right_support=13;valid_TSD=False
-##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
-##gff-version 3
 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