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57 lines
2.5 KiB
XML
57 lines
2.5 KiB
XML
<tool id="interactive_tool_wilson" tool_type="interactive" name="Wilson" version="0.1">
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<description>Webbased Interactive Omics visualization</description>
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<requirements>
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<container type="docker">loosolab/wilson:2.1.1</container>
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</requirements>
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<entry_points>
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<entry_point name="Wilson visualisation of $infile.display_name" requires_domain="True">
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<port>3838</port>
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</entry_point>
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</entry_points>
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<environment_variables>
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<environment_variable name="WILSON_LANDING_PAGE">feature_selection</environment_variable>
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<environment_variable name="WILSON_BLACKLIST_EXAMPLES">true</environment_variable>
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</environment_variables>
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<command><![CDATA[
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mkdir -p /srv/shiny-server/external_data/ &&
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echo "WILSON_LANDING_PAGE=\$WILSON_LANDING_PAGE" > /home/shiny/.Renviron &&
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echo "WILSON_BLACKLIST_EXAMPLES=\$WILSON_BLACKLIST_EXAMPLES" >> /home/shiny/.Renviron &&
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ln -s ${infile} /srv/shiny-server/external_data/input.clarion &&
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exec shiny-server 2>&1
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]]>
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</command>
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<inputs>
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<param name="infile" type="data" format="tabular,txt" label="Tabular in Clarion format"/>
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</inputs>
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<outputs>
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<data name="outfile" format="txt" />
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</outputs>
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<tests>
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</tests>
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<help>
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<![CDATA[
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`WIlsON: Webbased Interactive Omics visualizatioN <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki>`_
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.. class:: infomark
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Wilson uses the CLARION file format, which is a generic file format for quantitative comparisons of high throughput screens.
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CLARION is a data format specially developed to be used with Wilson, which relies on a tab-delimited table with
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a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports
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all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes)
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with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq,
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ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible
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without having to modify the code of Wilson for each specific experiment.
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Please check the following link for details considering the `CLARION format <https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format>`_.
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]]>
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</help>
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<citations>
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<citation type="doi">10.1093/bioinformatics/bty711</citation>
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</citations>
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</tool>
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