# HG changeset patch
# User mvdbeek
# Date 1494348850 14400
# Node ID 2c62ca47c4551904ee86e4d591c89da43006222d
# Parent  be95c9c82937e47113f4da0b1a0b52040deffcd5
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cbe482b98ef1dd753da7ffbc1fad7ba93f79ecc0-dirty

diff -r be95c9c82937 -r 2c62ca47c455 add_matesequence.xml
--- a/add_matesequence.xml	Tue May 09 10:38:06 2017 -0400
+++ b/add_matesequence.xml	Tue May 09 12:54:10 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.3.22">
+<tool id="add_matesequence" name="Add matesequence" version="0.3.23">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.3.22">readtagger</requirement>
+        <requirement type="package" version="0.3.23">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r be95c9c82937 -r 2c62ca47c455 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Tue May 09 10:38:06 2017 -0400
+++ b/allow_dovetailing.xml	Tue May 09 12:54:10 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.22">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.23">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.22">readtagger</requirement>
+        <requirement type="package" version="0.3.23">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r be95c9c82937 -r 2c62ca47c455 bam_readtagger.xml
--- a/bam_readtagger.xml	Tue May 09 10:38:06 2017 -0400
+++ b/bam_readtagger.xml	Tue May 09 12:54:10 2017 -0400
@@ -1,16 +1,19 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.22">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.23">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.22">readtagger</requirement>
+        <requirement type="package" version="0.3.23">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
@@ -30,6 +33,7 @@
                 <expand macro="tag_options"/>
             </param>
         </repeat>
+        <param argument="--reference_fasta" type="data" format="fasta" label="Reference fasta for realigning clipped reads" optional="True" help="This file is optional. If you provide it, clipped sequences are extracted and aligned against this fasta file."/>
         <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"/>
diff -r be95c9c82937 -r 2c62ca47c455 findcluster.xml
--- a/findcluster.xml	Tue May 09 10:38:06 2017 -0400
+++ b/findcluster.xml	Tue May 09 12:54:10 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.3.22">
+<tool id="findcluster" name="Find clusters of reads" version="0.3.23">
     <description>in bam files</description>
     <requirements>
-        <requirement type="package" version="0.3.22">readtagger</requirement>
+        <requirement type="package" version="0.3.23">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r be95c9c82937 -r 2c62ca47c455 update_mapq.xml
--- a/update_mapq.xml	Tue May 09 10:38:06 2017 -0400
+++ b/update_mapq.xml	Tue May 09 12:54:10 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.3.22">
+<tool id="update_mapq" name="Update MAPQ score" version="0.3.23">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.3.22">readtagger</requirement>
+        <requirement type="package" version="0.3.23">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r be95c9c82937 -r 2c62ca47c455 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Tue May 09 10:38:06 2017 -0400
+++ b/write_supplementary_fastq.xml	Tue May 09 12:54:10 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.22">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.23">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.3.22">readtagger</requirement>
+        <requirement type="package" version="0.3.23">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[