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view bum.xml @ 0:e41ec5af7472 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
author | iuc |
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date | Thu, 02 Aug 2018 11:57:44 -0400 |
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<tool id="heinz_bum" name="Fit a BUM model" version="1.0"> <description>with p-values</description> <requirements> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.34.0">bioconductor-bionet</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/bum.R' --input '$p_values' --output '$dist_params' ]]></command> <inputs> <param type="data" name="p_values" label="Input file" format="txt" help=" The input file should only contain p-values, one per line." /> </inputs> <outputs> <data name="dist_params" format="txt" label="${tool.name} on ${on_string}: BUM params"/> </outputs> <tests> <!--Ensure the stochastic result is similar enough--> <test> <param name="p_values" value="BUM_input.txt" /> <output name="dist_params"> <assert_contents> <has_text text="0.684" /> <has_text text="0.376" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ BUM is the abbreviation for "Beta-Uniform Mixture (BUM) distribution." This tool (part of the package "Bionet") is used for fitting Beta-Uniform mixture model to a P-value distribution, the output of which is two model parameters: lambda and alpha, kept in a text file, the first line is lambda; the second, alpha. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btq089</citation> <citation type="doi">10.1093/bioinformatics/btn161</citation> </citations> </tool>