# HG changeset patch
# User mvdbeek
# Date 1494340686 14400
# Node ID be95c9c82937e47113f4da0b1a0b52040deffcd5
# Parent  9f7737be4732903ea610709786bd5d6c8ffce5f3
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba-dirty

diff -r 9f7737be4732 -r be95c9c82937 add_matesequence.xml
--- a/add_matesequence.xml	Fri Apr 28 02:16:42 2017 -0400
+++ b/add_matesequence.xml	Tue May 09 10:38:06 2017 -0400
@@ -1,11 +1,11 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.21">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.22">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.21">readtagger</requirement>
+        <requirement type="package" version="0.3.22">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        add_matesequence --file_to_annotate '$file_to_annotate' --annotate_source '$annotate_source' --output_path '$output'
+        add_matesequence --target '$file_to_annotate' --source '$annotate_source' --output_path '$output'
     ]]></command>
     <inputs>
         <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/>
diff -r 9f7737be4732 -r be95c9c82937 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Fri Apr 28 02:16:42 2017 -0400
+++ b/allow_dovetailing.xml	Tue May 09 10:38:06 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.21">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.22">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.21">readtagger</requirement>
+        <requirement type="package" version="0.3.22">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 9f7737be4732 -r be95c9c82937 bam_readtagger.xml
--- a/bam_readtagger.xml	Fri Apr 28 02:16:42 2017 -0400
+++ b/bam_readtagger.xml	Tue May 09 10:38:06 2017 -0400
@@ -1,18 +1,18 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.21">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.22">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.21">readtagger</requirement>
+        <requirement type="package" version="0.3.22">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        readtagger -t '$tag_file' -a
+        readtagger -t '$tag_file' -s
         #for $element in $alignment_series
             '$element.annotate_with':$element.r_tag:$element.m_tag
         #end for
         $allow_dovetailing
-        $keep_suboptimal
+        $discard_suboptimal
         $discarded
         $verified
         $discard_proper_pairs
@@ -30,11 +30,11 @@
                 <expand macro="tag_options"/>
             </param>
         </repeat>
-        <param argument="--allow_dovetailing" type="boolean" truevalue="-d" falsevalue="" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
-        <param argument="-k" name="keep_suboptimal" type="boolean" truevalue="-k" falsevalue="" label="Keep suboptimal alternative tags" help="Check this to also keep alternative tags that cannot explain the current read cigar"/>
-        <param argument="-dp" name="discard_proper_pairs" type="boolean" truevalue="-dp" falsevalue="" label="Discard alternative tags for proper pairs" help="Check this to discard alternative tags for reads in proper pairs"/>
-        <param argument="-wd" name="discarded" type="boolean" truevalue="-wd discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
-        <param argument="-wv" name="verified" type="boolean" truevalue="-wv verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
+        <param argument="--allow_dovetailing" type="boolean" truevalue="--allow_dovetailing" falsevalue="--no_allow_dovetailing" checked="True" label="Allow dovetailing" help="Check this to label reads as proper_pair even if the mates of a pair overlap each other"/>
+        <param argument="--discard_suboptimal_alternate_tags" name="discard_suboptimal" type="boolean" checked="True" truevalue="--discard_suboptimal_alternate_tags" falsevalue="--no_discard_suboptimal" label="Discard suboptimal alternative tags" help="Check this to discard alternative tags that cannot explain the current read cigar"/>
+        <param argument="--discard_if_proper_pair" name="discard_proper_pairs" type="boolean" truevalue="--discard_if_proper_pair" falsevalue="--no_discard_if_proper_pair" label="Discard alternative tags for proper pairs" checked="True" help="Check this to discard alternative tags for reads in proper pairs"/>
+        <param argument="--discarded_path" name="discarded" type="boolean" truevalue="--discarded_path discarded.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that failed validation"/>
+        <param argument="--verified_path" name="verified" type="boolean" truevalue="--verified_path verified.bam" falsevalue="" label="Check this to produce an output file containing only the reads with tags that pass validation"/>
     </inputs>
     <outputs>
         <data name="tagged_file" format="bam" label="Tagged reads on $on_string"/>
diff -r 9f7737be4732 -r be95c9c82937 findcluster.xml
--- a/findcluster.xml	Fri Apr 28 02:16:42 2017 -0400
+++ b/findcluster.xml	Tue May 09 10:38:06 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.21">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.22">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.21">readtagger</requirement>
+        <requirement type="package" version="0.3.22">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 9f7737be4732 -r be95c9c82937 update_mapq.xml
--- a/update_mapq.xml	Fri Apr 28 02:16:42 2017 -0400
+++ b/update_mapq.xml	Tue May 09 10:38:06 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.21">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.22">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.21">readtagger</requirement>
+        <requirement type="package" version="0.3.22">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 9f7737be4732 -r be95c9c82937 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Fri Apr 28 02:16:42 2017 -0400
+++ b/write_supplementary_fastq.xml	Tue May 09 10:38:06 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.21">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.22">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.21">readtagger</requirement>
+        <requirement type="package" version="0.3.22">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[