# HG changeset patch
# User mvdbeek
# Date 1510228137 18000
# Node ID e19ff7992765b50bfbb5216851bfcfb0a332e896
# Parent  5aa7745dd6e3ba29660daffd352c447f790573ac
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty

diff -r 5aa7745dd6e3 -r e19ff7992765 add_matesequence.xml
--- a/add_matesequence.xml	Wed Jun 21 09:57:31 2017 -0400
+++ b/add_matesequence.xml	Thu Nov 09 06:48:57 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.25">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.0">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.25">readtagger</requirement>
+        <requirement type="package" version="0.4.0">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5aa7745dd6e3 -r e19ff7992765 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Wed Jun 21 09:57:31 2017 -0400
+++ b/allow_dovetailing.xml	Thu Nov 09 06:48:57 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.25">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.0">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.25">readtagger</requirement>
+        <requirement type="package" version="0.4.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 5aa7745dd6e3 -r e19ff7992765 bam_readtagger.xml
--- a/bam_readtagger.xml	Wed Jun 21 09:57:31 2017 -0400
+++ b/bam_readtagger.xml	Thu Nov 09 06:48:57 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.25">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.0">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.25">readtagger</requirement>
+        <requirement type="package" version="0.4.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 5aa7745dd6e3 -r e19ff7992765 deploy.sh
diff -r 5aa7745dd6e3 -r e19ff7992765 findcluster.xml
--- a/findcluster.xml	Wed Jun 21 09:57:31 2017 -0400
+++ b/findcluster.xml	Thu Nov 09 06:48:57 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.25">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.0">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.25">readtagger</requirement>
+        <requirement type="package" version="0.4.0">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -16,14 +16,14 @@
             #if str($transposon_source.reference_source_selector) == "history":
                 --transposon_reference_fasta '$transposon_source.ref_file'
             #else :
-                --transposon_bwa_index '$transposon_source.ref_file.fields.path'
+                --transposon_bwa_index '$reference_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 '$genome_source.ref_file'
             #else :
-                --genome_bwa_index '$genome_source.ref_file.fields.path'
+                --genome_bwa_index '$reference_source.ref_file.fields.path'
             #end if
         #end if
         --output_bam '$output_bam'
diff -r 5aa7745dd6e3 -r e19ff7992765 update_mapq.xml
--- a/update_mapq.xml	Wed Jun 21 09:57:31 2017 -0400
+++ b/update_mapq.xml	Thu Nov 09 06:48:57 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.25">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.0">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.25">readtagger</requirement>
+        <requirement type="package" version="0.4.0">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 5aa7745dd6e3 -r e19ff7992765 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Wed Jun 21 09:57:31 2017 -0400
+++ b/write_supplementary_fastq.xml	Thu Nov 09 06:48:57 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.25">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.0">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.25">readtagger</requirement>
+        <requirement type="package" version="0.4.0">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[