# HG changeset patch
# User mvdbeek
# Date 1511193042 18000
# Node ID 240c901dedc03ee182ba4edb8a035daafc08e748
# Parent  c7f140920cc13f9158cd3954b883368db4986234
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty

diff -r c7f140920cc1 -r 240c901dedc0 add_matesequence.xml
--- a/add_matesequence.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/add_matesequence.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="add_matesequence" name="Add matesequence" version="0.4.0">
+<tool id="add_matesequence" name="Add matesequence" version="0.4.1">
     <description>into tag field</description>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <version_command>add_matesequence --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r c7f140920cc1 -r 240c901dedc0 allow_dovetailing.xml
--- a/allow_dovetailing.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/allow_dovetailing.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.0">
+<tool id="allow_dovetailing" name="Allow dovetailing" version="0.4.1">
     <description>modifies proper_pair flag in bam files</description>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         allow_dovetailing -i '$input' -o '$output'
diff -r c7f140920cc1 -r 240c901dedc0 bam_readtagger.xml
--- a/bam_readtagger.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/bam_readtagger.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.0">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.1">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -s
diff -r c7f140920cc1 -r 240c901dedc0 findcluster.xml
--- a/findcluster.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/findcluster.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,13 +1,15 @@
-<tool id="findcluster" name="Find clusters of reads" version="0.4.0">
+<tool id="findcluster" name="Find clusters of reads" version="0.4.1">
     <description>in bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+        #import re
+        #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
         ln -f -s $input input.bam &&
         ln -f -s $input.metadata.bam_index input.bam.bai &&
         findcluster
@@ -29,7 +31,7 @@
         --output_bam '$output_bam'
         --output_gff '$output_gff'
         --output_fasta '$output_fasta'
-        --sample_name '$input.element_identifier'
+        --sample_name '$sample_name'
         --threads "\${GALAXY_SLOTS:-2}"
     ]]></command>
     <inputs>
diff -r c7f140920cc1 -r 240c901dedc0 plot_coverage.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_coverage.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -0,0 +1,40 @@
+<tool id="plot_coverage" name="Plot coverage" version="0.4.1">
+    <description>as area plot between BAM files</description>
+    <requirements>
+        <requirement type="package" version="0.4.1">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'
+    ]]></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"/>
+        <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">
+                    <add value="-" />
+                    <add value="," />
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
+    </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="regions" value="3R:13373525-13373615"/>
+            <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+This tool plots the coverage over a specified region (by default all chromosomes/contigs).
+
+    ]]></help>
+</tool>
diff -r c7f140920cc1 -r 240c901dedc0 test-data/three_cluster_plot.pdf
Binary file test-data/three_cluster_plot.pdf has changed
diff -r c7f140920cc1 -r 240c901dedc0 update_mapq.xml
--- a/update_mapq.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/update_mapq.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="update_mapq" name="Update MAPQ score" version="0.4.0">
+<tool id="update_mapq" name="Update MAPQ score" version="0.4.1">
     <description>of supplementary alignments</description>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <version_command>update_mapq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
diff -r c7f140920cc1 -r 240c901dedc0 write_supplementary_fastq.xml
--- a/write_supplementary_fastq.xml	Thu Nov 09 06:49:15 2017 -0500
+++ b/write_supplementary_fastq.xml	Mon Nov 20 10:50:42 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.0">
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.4.1">
     <description>from SAM/BAM alignment files as FASTQ</description>
     <requirements>
-        <requirement type="package" version="0.4.0">readtagger</requirement>
+        <requirement type="package" version="0.4.1">readtagger</requirement>
     </requirements>
     <version_command>write_supplementary_fastq --version</version_command>
     <command detect_errors="aggressive"><![CDATA[