# HG changeset patch
# User mvdbeek
# Date 1513241524 18000
# Node ID 02afdbc69591f886ec3bf9d63e817abc9496aa03
# Parent  240c901dedc03ee182ba4edb8a035daafc08e748
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e4cd04d8a19b57d6b23da64c3fda8978b51e33ef

diff -r 240c901dedc0 -r 02afdbc69591 add_matesequence.xml
--- a/add_matesequence.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/add_matesequence.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.1">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.4">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 240c901dedc0 -r 02afdbc69591 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/allow_dovetailing.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.1">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.4">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 240c901dedc0 -r 02afdbc69591 bam_readtagger.xml
--- a/bam_readtagger.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/bam_readtagger.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.1">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.4">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 240c901dedc0 -r 02afdbc69591 deploy.sh
diff -r 240c901dedc0 -r 02afdbc69591 findcluster.xml
--- a/findcluster.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/findcluster.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.1">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.4">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -18,14 +18,14 @@
             #if str($transposon_source.reference_source_selector) == "history":
                 --transposon_reference_fasta '$transposon_source.ref_file'
             #else :
-                --transposon_bwa_index '$reference_source.ref_file.fields.path'
+                --transposon_bwa_index '$transposon_source.ref_file.fields.path'
             #end if
         #end if
         #if $genome_source.ref_file:
             #if str($genome_source.reference_source_selector) == "history":
                 --genome_reference_fasta '$genome_source.ref_file'
             #else :
-                --genome_bwa_index '$reference_source.ref_file.fields.path'
+                --genome_bwa_index '$genome_source.ref_file.fields.path'
             #end if
         #end if
         --output_bam '$output_bam'
diff -r 240c901dedc0 -r 02afdbc69591 plot_coverage.xml
--- a/plot_coverage.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/plot_coverage.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.1">
+<tool id="plot_coverage" name="Plot coverage" version="0.4.4">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 240c901dedc0 -r 02afdbc69591 test-data/three_cluster_plot.pdf
Binary file test-data/three_cluster_plot.pdf has changed
diff -r 240c901dedc0 -r 02afdbc69591 update_mapq.xml
--- a/update_mapq.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/update_mapq.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.1">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.4">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 240c901dedc0 -r 02afdbc69591 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Mon Nov 20 10:50:42 2017 -0500
+++ b/write_supplementary_fastq.xml	Thu Dec 14 03:52:04 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.1">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.4">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.1">readtagger</requirement>
+        <requirement type="package" version="0.4.4">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[