Mercurial > repos > bgruening > bismark
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'
author | bgruening |
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date | Sat, 06 May 2017 13:18:09 -0400 |
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--- /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>