diff bismark_methylation_extractor.xml @ 22:8c191acde702 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35

--- 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>