diff bismark_pretty_report/bismark2report_wrapper.xml @ 7:fcadce4d9a06 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_pretty_report/bismark2report_wrapper.xml	Sat May 06 13:18:09 2017 -0400
@@ -0,0 +1,75 @@
+<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.16.3">
+
+    <description>Generates a graphical HTML report page from report outputs of Bismark</description>
+    <!--<version_command>bismark version</version_command>-->
+
+    <requirements>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+
+    <command interpreter="python">
+<![CDATA[
+        bismark2report_wrapper.py
+
+        --tool_dir "$__tool_directory__"
+
+        --alignment_report "$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 $output_html_report
+        --output_html_report_link "$output_html_report_link"
+        --output_dir "$output_html_report_link.files_path"
+
+        ##--log_report $log_report
+]]>
+    </command>
+
+    <inputs>
+        <param name="alignment" type="data" format="txt" label="Submit a Bismark mapping report" optional="False"/>
+        <section name="additional_reports" title="Additional reports to include in the HTML page (optional)" expanded="True">
+            <param name="dedup" type="data" format="txt" label="Submit the corresponding Bismark deduplication report" optional="True" help="Optional output of the module *Bismark Deduplicate*"/>
+            <param name="splitting" type="data" format="txt" label="Submit the corresponding Bismark splitting report" optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
+            <param name="mbias" type="data" format="txt" label="Submit the corresponding Bismark M-bias report" optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
+            <param name="nucleotide" type="data" format="txt" label="Submit the corresponding Bismark nucleotide report" optional="True" help="Optional output of the module *Bismark Mapping*"/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <!--<data name="output_html_report" format="html" label="${tool.name} on ${on_string}: Download pretty html report"/>-->
+        <data name="output_html_report_link" format="html" label="${tool.name} on ${on_string}: Visualize pretty html report"/>
+        <!--<data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)"/>-->
+    </outputs>
+
+    <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>