# HG changeset patch
# User mvdbeek
# Date 1527174338 14400
# Node ID 4fdf606153df8c287d962b420f5548059300fb15
# Parent  4b1ebfcd0f466a58c2f02f175ca55156d2c6a50d
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty

diff -r 4b1ebfcd0f46 -r 4fdf606153df add_matesequence.xml
--- a/add_matesequence.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/add_matesequence.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.10">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.11">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 4b1ebfcd0f46 -r 4fdf606153df allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/allow_dovetailing.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.10">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.11">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 4b1ebfcd0f46 -r 4fdf606153df bam_readtagger.xml
--- a/bam_readtagger.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/bam_readtagger.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.10">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.11">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 4b1ebfcd0f46 -r 4fdf606153df filter_insertions.xml
--- a/filter_insertions.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/filter_insertions.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.11">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -11,14 +11,16 @@
         confirm_insertions
         --putative_insertions_path putative_insertions.gff
         --all_treatments_path all_insertions.gff
-        --all_controls_path all_controls_path.gff
+        #for p in $all_controls
+            --all_controls_paths '$p'
+        #end for
         --output_path '$output'
         $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 control sample" argument="--all_controls_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="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 4b1ebfcd0f46 -r 4fdf606153df findcluster.xml
--- a/findcluster.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/findcluster.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.10">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.11">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 4b1ebfcd0f46 -r 4fdf606153df plot_coverage.xml
--- a/plot_coverage.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/plot_coverage.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.10">
+<tool id="plot_coverage" name="Plot coverage" version="0.4.11">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 4b1ebfcd0f46 -r 4fdf606153df test-data/extended_and_annotated_roi.bam.bai
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
diff -r 4b1ebfcd0f46 -r 4fdf606153df test-data/out.png
Binary file test-data/out.png has changed
diff -r 4b1ebfcd0f46 -r 4fdf606153df test-data/three_cluster_out.bam.bai
Binary file test-data/three_cluster_out.bam.bai has changed
diff -r 4b1ebfcd0f46 -r 4fdf606153df update_mapq.xml
--- a/update_mapq.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/update_mapq.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.10">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.11">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 4b1ebfcd0f46 -r 4fdf606153df write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/write_supplementary_fastq.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.10">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.11">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[