# HG changeset patch
# User mvdbeek
# Date 1547489870 18000
# Node ID c2104094afd384bf263cd8708df76cd6fbafd693
# Parent  fbfd1082de711376e5cd6ade52f2ac77221fb432
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit ae40519a953219ec4cc8ef4d586fc06cad88fb01

diff -r fbfd1082de71 -r c2104094afd3 add_matesequence.xml
--- a/add_matesequence.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/add_matesequence.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.12">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.13">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r fbfd1082de71 -r c2104094afd3 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/allow_dovetailing.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.12">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.13">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r fbfd1082de71 -r c2104094afd3 bam_readtagger.xml
--- a/bam_readtagger.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/bam_readtagger.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,31 +1,31 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.13">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-readtagger -t '$tag_file' -s
-#for $element in $alignment_series
-    '$element.annotate_with':$element.r_tag:$element.m_tag
-#end for
-#if $reference_fasta:
-    --reference_fasta '$reference_fasta'
-#end if
-$allow_dovetailing
-$discard_suboptimal
-$discarded
-$verified
-$discard_proper_pairs
---cores "\${GALAXY_SLOTS:-2}"
--o '$tagged_file'
+        readtagger -t '$tag_file' -s
+        #for $element in $alignment_series
+            '$element.annotate_with':$element.r_tag:$element.m_tag
+        #end for
+        #if $reference_fasta:
+            --reference_fasta '$reference_fasta'
+        #end if
+        $allow_dovetailing
+        $discard_suboptimal
+        $discarded
+        $verified
+        $discard_proper_pairs
+        --cores "\${GALAXY_SLOTS:-2}"
+        -o '$tagged_file'
     ]]></command>
     <inputs>
-        <param name="tag_file" argument="--tag_file" type="data" format="qname_sorted.bam,bam"/>
+        <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
         <repeat name="alignment_series" title="Alignments">
-            <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/>
+            <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
             <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
                 <expand macro="tag_options"/>
             </param>
diff -r fbfd1082de71 -r c2104094afd3 filter_insertions.xml
--- a/filter_insertions.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/filter_insertions.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.12">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.13">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r fbfd1082de71 -r c2104094afd3 findcluster.xml
--- a/findcluster.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/findcluster.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.12">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.13">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r fbfd1082de71 -r c2104094afd3 plot_coverage.xml
--- a/plot_coverage.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/plot_coverage.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.4.12">
+<tool id="plot_coverage" name="Plot coverage" version="0.4.13">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r fbfd1082de71 -r c2104094afd3 test-data/extended_and_annotated_roi.bam.bai
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
diff -r fbfd1082de71 -r c2104094afd3 test-data/out.png
Binary file test-data/out.png has changed
diff -r fbfd1082de71 -r c2104094afd3 test-data/three_cluster_out.bam.bai
Binary file test-data/three_cluster_out.bam.bai has changed
diff -r fbfd1082de71 -r c2104094afd3 update_mapq.xml
--- a/update_mapq.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/update_mapq.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.12">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.13">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r fbfd1082de71 -r c2104094afd3 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/write_supplementary_fastq.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.12">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.13">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[