Mercurial > repos > mvdbeek > bam_readtagger

diff plot_coverage.xml @ 78:6178c24ddd5a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
author mvdbeek
date Tue, 07 Apr 2020 08:57:47 -0400
parents b9b76f9a816c
children c42dd2551c9c
line wrap: on
line diff
--- a/plot_coverage.xml	Tue Mar 24 07:23:30 2020 -0400
+++ b/plot_coverage.xml	Tue Apr 07 08:57:47 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="plot_coverage" name="Plot coverage" version="0.5.23">
+<tool id="plot_coverage" name="Plot coverage" version="0.5.24">
     <description>as area plot between BAM files</description>
     <requirements>
-        <requirement type="package" version="0.5.23">readtagger</requirement>
+        <requirement type="package" version="0.5.24">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 #import re
@@ -10,7 +10,7 @@
     #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'
+output.pdf --cores \${GALAXY_SLOTS:-4} --regions '$regions' --plot_kind $plot_kind
     ]]></command>
     <inputs>
         <repeat name="input_files" title="Add input files to coverage plot" min="1">
@@ -27,6 +27,10 @@
                 </valid>
             </sanitizer>
         </param>
+        <param name="plot_kind" type="select" label="Select the plot type">
+            <option value="area">Area plot</option>
+            <option value="line">Line plot</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="pdf" label="Coverage plot on $on_string" from_work_dir="output.pdf"/>
@@ -40,6 +44,15 @@
             <param name="regions" value="3R:13373525-13373615"/>
             <output name="output" file="three_cluster_plot.pdf" ftype="pdf" compare="sim_size"/>
         </test>
+        <test>
+            <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"/>
+            <param name="plot_kind" value="line"/>
+            <output name="output" file="three_cluster_plot_line.pdf" ftype="pdf" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[