# HG changeset patch
# User mvdbeek
# Date 1584973442 14400
# Node ID 2c7f70390b7c226514ddbd102d823066ebef9153
# Parent  6c15dd4415ea1e26e28ee600e9bf9deb942cc272
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8ee42193ec9c4778fd2bd312f53322389b0731c5"

diff -r 6c15dd4415ea -r 2c7f70390b7c add_matesequence.xml
--- a/add_matesequence.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/add_matesequence.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.5.21">
+<tool id="add_matesequence" name="Add matesequence" version="0.5.22">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 6c15dd4415ea -r 2c7f70390b7c allow_dovetailing.xml
--- a/allow_dovetailing.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/allow_dovetailing.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.21">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.5.22">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r 6c15dd4415ea -r 2c7f70390b7c bam_readtagger.xml
--- a/bam_readtagger.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/bam_readtagger.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.5.21">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.5.22">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r 6c15dd4415ea -r 2c7f70390b7c extract_variants.xml
--- a/extract_variants.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/extract_variants.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.21">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.22">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 6c15dd4415ea -r 2c7f70390b7c filter_insertions.xml
--- a/filter_insertions.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/filter_insertions.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.21">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.5.22">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 6c15dd4415ea -r 2c7f70390b7c findcluster.xml
--- a/findcluster.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/findcluster.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,10 +1,10 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.5.21">
+<tool id="findcluster" name="Find clusters of reads" version="0.5.22">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 6c15dd4415ea -r 2c7f70390b7c normalize_readsizes.xml
--- a/normalize_readsizes.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/normalize_readsizes.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.21">
+<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.22">
     <description>of multiple fastq files</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>normalize_readsizes --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 6c15dd4415ea -r 2c7f70390b7c plot_coverage.xml
--- a/plot_coverage.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/plot_coverage.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,17 +1,22 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.21">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.22">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        #import re
-        #set identifier1 = re.sub('[^\w\-_\.\,]', '_', str( $input1.element_identifier))
-        #set identifier2 = re.sub('[^\w\-_\.\,]', '_', str( $input2.element_identifier))
-        plot_coverage '$input1' '$identifier1' '$input2' '$identifier2' output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
+#import re
+plot_coverage
+#for $r in $input_files
+    #set identifier = re.sub('[^\w\-_\.\,]', '_', str( $r.input.element_identifier))
+    --file '$r.input' '$identifier' $r.total_reads
+#end for
+output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions'
     ]]></command>
     <inputs>
-        <param name="input1" type="data" format="bam,cram" label="Select a BAM file to plot"/>
-        <param name="input2" type="data" format="bam,cram" label="Select a second BAM file to plot" optional="true"/>
+        <repeat name="input_files" title="Add input files to coverage plot" min="1">
+            <param name="input" type="data" format="bam,cram" label="Select a BAM file to plot"/>
+            <param name="total_reads" type="integer" value="0" min="0" label="Total number of (mapped) reads. If given plot scale will be reads per million"/>
+        </repeat>
         <param name="regions" type="text" label="Select regions to plot" optional="true" help="e.g X:1200000-1250000,X1250000-1300000. If left blank will plot all contigs/chromosomes.">
             <sanitizer>
                 <valid initial="string.letters,string.digits">
@@ -27,8 +32,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="three_cluster_out.bam" ftype="bam"/>
-            <param name="input2" value="three_cluster_out.bam" ftype="bam"/>
+            <param name="input_files_0|input" value="three_cluster_out.bam" ftype="bam"/>
+            <param name="input_files_1|input" value="three_cluster_out.bam" ftype="bam"/>
+            <param name="input_files_0|total_reads" value="1000000" ftype="bam"/>
+            <param name="input_files_1|total_reads" value="1000000" ftype="bam"/>
             <param name="regions" value="3R:13373525-13373615"/>
             <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
         </test>
diff -r 6c15dd4415ea -r 2c7f70390b7c test-data/three_cluster_plot.pdf
Binary file test-data/three_cluster_plot.pdf has changed
diff -r 6c15dd4415ea -r 2c7f70390b7c update_mapq.xml
--- a/update_mapq.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/update_mapq.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.5.21">
+<tool id="update_mapq" name="Update MAPQ score" version="0.5.22">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r 6c15dd4415ea -r 2c7f70390b7c write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Mon Jan 13 10:10:10 2020 -0500
+++ b/write_supplementary_fastq.xml	Mon Mar 23 10:24:02 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.21">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.22">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.5.21">readtagger</requirement>
+        <requirement type="package" version="0.5.22">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[