# HG changeset patch
# User mvdbeek
# Date 1540548614 14400
# Node ID fbfd1082de711376e5cd6ade52f2ac77221fb432
# Parent  29734dbad6de1bcaac0b23a001d8563355333d7e
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 7ee4c1dd4e13a4d634b0e80efdd2309289a29a1c

diff -r 29734dbad6de -r fbfd1082de71 add_matesequence.xml
--- a/add_matesequence.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/add_matesequence.xml	Fri Oct 26 06:10:14 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="0.4.12">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 29734dbad6de -r fbfd1082de71 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/allow_dovetailing.xml	Fri Oct 26 06:10:14 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="0.4.12">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 29734dbad6de -r fbfd1082de71 bam_readtagger.xml
--- a/bam_readtagger.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/bam_readtagger.xml	Fri Oct 26 06:10:14 2018 -0400
@@ -1,31 +1,31 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.10">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12">
     <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="0.4.12">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="bam"/>
+        <param name="tag_file" argument="--tag_file" type="data" format="qname_sorted.bam,bam"/>
         <repeat name="alignment_series" title="Alignments">
-            <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
+            <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/>
             <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
                 <expand macro="tag_options"/>
             </param>
diff -r 29734dbad6de -r fbfd1082de71 filter_insertions.xml
--- a/filter_insertions.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/filter_insertions.xml	Fri Oct 26 06:10:14 2018 -0400
@@ -1,24 +1,28 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.12">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
         ln -fs $putative_insertions putative_insertions.gff &&
         ln -fs $all_insertions all_insertions.gff &&
-        ln -fs $all_controls all_controls_path.gff &&
+        #for i, p in enumerate($all_controls)
+            ln -fs '$p' all_controls_${i}.gff &&
+        #end for
         confirm_insertions
         --putative_insertions_path putative_insertions.gff
         --all_treatments_path all_insertions.gff
-        --all_controls_path all_controls_path.gff
+        #for i, p in enumerate($all_controls)
+            --all_controls_paths all_controls_${i}.gff
+        #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 29734dbad6de -r fbfd1082de71 findcluster.xml
--- a/findcluster.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/findcluster.xml	Fri Oct 26 06:10:14 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="0.4.12">
     <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="0.4.12">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 29734dbad6de -r fbfd1082de71 plot_coverage.xml
--- a/plot_coverage.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/plot_coverage.xml	Fri Oct 26 06:10:14 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="0.4.12">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
diff -r 29734dbad6de -r fbfd1082de71 test-data/extended_and_annotated_roi.bam.bai
Binary file test-data/extended_and_annotated_roi.bam.bai has changed
diff -r 29734dbad6de -r fbfd1082de71 test-data/out.png
Binary file test-data/out.png has changed
diff -r 29734dbad6de -r fbfd1082de71 test-data/three_cluster_out.bam.bai
Binary file test-data/three_cluster_out.bam.bai has changed
diff -r 29734dbad6de -r fbfd1082de71 update_mapq.xml
--- a/update_mapq.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/update_mapq.xml	Fri Oct 26 06:10:14 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="0.4.12">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 29734dbad6de -r fbfd1082de71 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/write_supplementary_fastq.xml	Fri Oct 26 06:10:14 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="0.4.12">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[