# HG changeset patch
# User bgruening
# Date 1690890130 0
# Node ID 8c191acde7024b9fa03ea5009c4abc770bd4f193
# Parent  120b7b35e4428f4cd019deef254c15cad77efe72
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35

diff -r 120b7b35e442 -r 8c191acde702 bismark_methylation_extractor.py
--- a/bismark_methylation_extractor.py	Thu Apr 22 17:05:46 2021 +0000
+++ b/bismark_methylation_extractor.py	Tue Aug 01 11:42:10 2023 +0000
@@ -69,6 +69,8 @@
     parser.add_argument("--splitting_report", dest="splitting_report")
     parser.add_argument("--mbias_report", dest="mbias_report")
     parser.add_argument("--cytosine_report", dest="cytosine_report")
+    parser.add_argument("--coverage_file", dest="coverage_file")
+
     parser.add_argument("--genome_file", dest="genome_file")
     parser.add_argument("--cx_context", action="store_true")
 
@@ -133,7 +135,6 @@
                     "--bedGraph",
                     "--CX_context",
                     "--cytosine_report",
-                    "--CX_context",
                     "--genome_folder",
                     tmp_genome_dir,
                 ]
@@ -175,11 +176,20 @@
                 glob(os.path.join(output_dir, "*CX_report.txt"))[0],
                 args.cytosine_report,
             )
+
         else:
             shutil.move(
                 glob(os.path.join(output_dir, "*CpG_report.txt"))[0],
                 args.cytosine_report,
             )
+
+    # coverage file
+    if args.coverage_file:
+        shutil.move(
+            glob(os.path.join(output_dir, "*datbismark.cov.gz"))[0],
+            args.coverage_file,
+        )
+
     # splitting report
     if args.splitting_report:
         logger.debug("Collecting splitting report.")
diff -r 120b7b35e442 -r 8c191acde702 bismark_methylation_extractor.xml
--- a/bismark_methylation_extractor.xml	Thu Apr 22 17:05:46 2021 +0000
+++ b/bismark_methylation_extractor.xml	Tue Aug 01 11:42:10 2023 +0000
@@ -1,9 +1,9 @@
-<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1" profile="18.01">
+<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1+galaxy1" profile="18.01">
     <description>Reports on methylation status of reads mapped by Bismark</description>
     <requirements>
         <requirement type="package" version="0.22.1">bismark</requirement>
         <requirement type="package" version="1.8">samtools</requirement>
-        <requirement type="package" version="2.3.5">bowtie2</requirement>
+        <requirement type="package" version="2.4.4">bowtie2</requirement>
     </requirements>
     <command><![CDATA[
         python '$__tool_directory__/bismark_methylation_extractor.py'
@@ -45,6 +45,9 @@
 
         #if $cytosine_report['cytosine_report_selector']:
           --cytosine_report '$output_cytosine_report'
+          #if  $cytosine_report['coverage_output']:
+            --coverage_file '$coverage_file'
+          #end if
           #if $cytosine_report.refGenomeSource.genomeSource == "built_in_fasta":
             --genome_file '${cytosine_report.refGenomeSource.built_in_fasta.fields.path}'
           #else:
@@ -128,6 +131,9 @@
                 </conditional>
                 <param name="cpg_context" type="boolean" truevalue="true" falsevalue="false" checked="False"
                        label="Reports Cpg Context only"/>
+                <param name="coverage_output" type="boolean" truevalue="true" falsevalue="false" checked="False"
+                       label="Generate Bismark coverage report"/>
+                
             </when>
             <when value="false"></when>
         </conditional>
@@ -158,6 +164,10 @@
               label="${tool.name} on ${on_string}: Genome-wide methylation report.">
             <filter>( cytosine_report['cytosine_report_selector'] )</filter>
         </data>
+        <data format="tabular.gz" name="coverage_file"
+              label="${tool.name} on ${on_string}:Coverage file.">
+            <filter>( cytosine_report['cytosine_report_selector'] and cytosine_report['coverage_output'])</filter>
+        </data>
         <data format="zip" name="compressed_output" label="${tool.name} on ${on_string}: Result archive."/>
         <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
             <filter>( output_settings['separate_logfile'] is True )</filter>
@@ -184,6 +194,20 @@
                 </assert_contents>
             </output>
         </test>
+        <!--Test coverage output -->
+        <test>
+            <param name="input" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
+            <param name="sPaired" value="single"/>
+            <param name="cytosine_report_selector" value="true"/>
+            <param name="genomeSource" value="history"/>
+            <param name="own_file" value="mm10.tiny.fa.gz" />
+            <param name="coverage_output" value="true"/>
+            <output name="coverage_file" ftype="tabular.gz">
+                <assert_contents>
+                    <has_size value="19960" delta="300"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 
     <help>
diff -r 120b7b35e442 -r 8c191acde702 test-data/output_splitting_report.txt
--- a/test-data/output_splitting_report.txt	Thu Apr 22 17:05:46 2021 +0000
+++ b/test-data/output_splitting_report.txt	Tue Aug 01 11:42:10 2023 +0000
@@ -1,4 +1,4 @@
-dataset_76c1988f-01b0-427e-9dbe-bfb5eee1c664.dat
+dataset_4c47ea8c-d35c-4f79-9403-33b9e262c542.dat
 
 Parameters used to extract methylation information:
 Bismark Extractor Version: v0.22.1