# HG changeset patch
# User mvdbeek
# Date 1560363798 14400
# Node ID 54aafdb84833e16eec56f4abda343101856936a5
# Parent  21acaf15af892a43657f4f3f06b8884dfe5cfa29
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 45d0337e2a0d35e9a83d9c87c005c876c45ee054

diff -r 21acaf15af89 -r 54aafdb84833 add_matesequence.xml
--- a/add_matesequence.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/add_matesequence.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.17">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.0">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 21acaf15af89 -r 54aafdb84833 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/allow_dovetailing.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.17">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.0">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 21acaf15af89 -r 54aafdb84833 bam_readtagger.xml
--- a/bam_readtagger.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/bam_readtagger.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.17">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.0">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
@@ -23,9 +23,9 @@
         -o '$tagged_file'
     ]]></command>
     <inputs>
-        <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_input_sorted.bam"/>
+        <param name="tag_file" argument="--tag_file" type="data" format="bam,qname_sorted.bam"/>
         <repeat name="alignment_series" title="Alignments">
-            <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_input_sorted.bam"/>
+            <param name="annotate_with" argument="--annotate_with" type="data" format="bam,qname_sorted.bam"/>
             <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
                 <expand macro="tag_options"/>
             </param>
diff -r 21acaf15af89 -r 54aafdb84833 filter_insertions.xml
--- a/filter_insertions.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/filter_insertions.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.17">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.0">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -20,9 +20,9 @@
         $output_discard
     ]]></command>
     <inputs>
-        <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/>
-        <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
-        <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/>
+        <param name="putative_insertions" label="Select dataset with filtered putative insertions" argument="--putative_insertions_path" type="data" format="gff3"/>
+        <param name="all_insertions" label="Select datasets with all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/>
+        <param name="all_controls" label="Select datasets with all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/>
         <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/>
     </inputs>
     <outputs>
diff -r 21acaf15af89 -r 54aafdb84833 findcluster.xml
--- a/findcluster.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/findcluster.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.17">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.0">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 21acaf15af89 -r 54aafdb84833 plot_coverage.xml
--- a/plot_coverage.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/plot_coverage.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.17">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.0">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 21acaf15af89 -r 54aafdb84833 test-data/extended_and_annotated_roi.bam.bai
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
diff -r 21acaf15af89 -r 54aafdb84833 test-data/out.png
Binary file test-data/out.png has changed
diff -r 21acaf15af89 -r 54aafdb84833 test-data/three_cluster_out.bam.bai
Binary file test-data/three_cluster_out.bam.bai has changed
diff -r 21acaf15af89 -r 54aafdb84833 update_mapq.xml
--- a/update_mapq.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/update_mapq.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.17">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.0">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 21acaf15af89 -r 54aafdb84833 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sun Feb 10 15:58:36 2019 -0500
+++ b/write_supplementary_fastq.xml	Wed Jun 12 14:23:18 2019 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.17">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.0">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.17">readtagger</requirement>
+        <requirement type="package" version="0.5.0">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[