--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark2report_wrapper.xml	Wed Aug 22 08:09:42 2018 -0400
@@ -0,0 +1,81 @@
+<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.20.0" profile="17.01">
+    <description>Generates a graphical HTML report page from report outputs of Bismark</description>
+    <requirements>
+        <requirement type="package" version="0.20.0">bismark</requirement>
+        <requirement type="package" version="1.8">samtools</requirement>
+        <requirement type="package" version="2.3.4.2">bowtie2</requirement>
+    </requirements>
+    <command><![CDATA[
+        python '$__tool_directory__/bismark2report_wrapper.py'
+
+        --alignment_report '$alignment'
+
+        #if $additional_reports['dedup']:
+        	--dedup_report '$additional_reports["dedup"]'
+        #end if
+        #if $additional_reports['splitting']:
+            --splitting_report '$additional_reports["splitting"]'
+        #end if
+        #if $additional_reports['mbias']:
+            --mbias_report '$additional_reports["mbias"]'
+        #end if
+        #if $additional_reports['nucleotide']:
+            --nucleotide_report '$additional_reports["nucleotide"]'
+        #end if
+
+        --output_html_report '$output_html_report'
+
+        #if $separate_logfile:
+            --log_report '$log_report'
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="alignment" type="data" format="txt" label="Submit a Bismark mapping report" optional="False"/>
+        <section name="additional_reports" title="Additional reports to include in the HTML page (optional)"
+                 expanded="True">
+            <param name="dedup" type="data" format="txt" label="Submit the corresponding Bismark deduplication report"
+                   optional="True" help="Optional output of the module *Bismark Deduplicate*"/>
+            <param name="splitting" type="data" format="txt" label="Submit the corresponding Bismark splitting report"
+                   optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
+            <param name="mbias" type="data" format="txt" label="Submit the corresponding Bismark M-bias report"
+                   optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
+            <param name="nucleotide" type="data" format="txt" label="Submit the corresponding Bismark nucleotide report"
+                   optional="True" help="Optional output of the module *Bismark Mapping*"/>
+        </section>
+        <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
+               label="Create a separate logfile, otherwise logs are added to the dataset info."/>
+    </inputs>
+
+    <outputs>
+        <data name="output_html_report" format="html"
+              label="${tool.name} on ${on_string}: Download pretty html report"/>
+        <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
+            <filter>( separate_logfile is True )</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="alignment" value="mapping_report.txt" ftype="txt"/>
+            <param name="dedup" value="dedup_report.txt" ftype="txt"/>
+            <param name="splitting" value="output_splitting_report.txt" ftype="txt"/>
+            <param name="mbias" value="output_mbias_report.txt" ftype="txt"/>
+            <output name="output_html_report" file="output_html_report.html" ftype="html" lines_diff="8"/>
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+**What it does**
+
+    | This tool uses a Bismark alignment report to generate a graphical HTML report page.
+    | Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well.
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr167</citation>
+    </citations>
+</tool>