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annotate bum.xml @ 4:e520fbedf79b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:38:20 +0000
parents a365150d73c0
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a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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1 <tool id="heinz_bum" name="Fit a BUM model" version="1.0">
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2 <description>with p-values</description>
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e520fbedf79b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xrefs>
e520fbedf79b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xref type="bio.tools">bionet</xref>
e520fbedf79b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 </xrefs>
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a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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6 <requirements>
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7 <requirement type="package" version="1.20.0">r-getopt</requirement>
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8 <requirement type="package" version="1.34.0">bioconductor-bionet</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript '$__tool_directory__/bum.R' --input '$p_values' --output '$dist_params'
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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12 ]]></command>
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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13 <inputs>
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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14 <param type="data" name="p_values" label="Input file" format="txt" help="
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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15 The input file should only contain p-values, one per line." />
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16 </inputs>
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17 <outputs>
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18 <data name="dist_params" format="txt" label="${tool.name} on ${on_string}: BUM params"/>
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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19 </outputs>
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20 <tests>
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21 <!--Ensure the stochastic result is similar enough-->
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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22 <test>
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23 <param name="p_values" value="BUM_input.txt" />
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24 <output name="dist_params">
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25 <assert_contents>
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26 <has_text text="0.684" />
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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27 <has_text text="0.376" />
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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28 </assert_contents>
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29 </output>
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30 </test>
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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31 </tests>
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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32 <help><![CDATA[
a365150d73c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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33 BUM is the abbreviation for "Beta-Uniform Mixture (BUM) distribution."
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34
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35 This tool (part of the package "Bionet") is used for fitting Beta-Uniform
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36 mixture model to a P-value distribution, the output of which is two model
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37 parameters: lambda and alpha, kept in a text file, the first line is
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38 lambda; the second, alpha.
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39 ]]></help>
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40 <citations>
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41 <citation type="doi">10.1093/bioinformatics/btq089</citation>
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42 <citation type="doi">10.1093/bioinformatics/btn161</citation>
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43 </citations>
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44 </tool>