Mercurial > repos > iuc > heinz
annotate bum.xml @ 3:2b80a2596064 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit 8007f71281553ddfa45e6f8e1172952d956bb000"
author | iuc |
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date | Thu, 11 Jun 2020 07:18:17 -0400 |
parents | e41ec5af7472 |
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e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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1 <tool id="heinz_bum" name="Fit a BUM model" version="1.0"> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
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2 <description>with p-values</description> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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3 <requirements> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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4 <requirement type="package" version="1.20.0">r-getopt</requirement> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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5 <requirement type="package" version="1.34.0">bioconductor-bionet</requirement> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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6 </requirements> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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7 <command detect_errors="exit_code"><![CDATA[ |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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8 Rscript '$__tool_directory__/bum.R' --input '$p_values' --output '$dist_params' |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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9 ]]></command> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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10 <inputs> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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11 <param type="data" name="p_values" label="Input file" format="txt" help=" |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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12 The input file should only contain p-values, one per line." /> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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13 </inputs> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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14 <outputs> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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15 <data name="dist_params" format="txt" label="${tool.name} on ${on_string}: BUM params"/> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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16 </outputs> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
parents:
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17 <tests> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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18 <!--Ensure the stochastic result is similar enough--> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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19 <test> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
parents:
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20 <param name="p_values" value="BUM_input.txt" /> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
parents:
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21 <output name="dist_params"> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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22 <assert_contents> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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23 <has_text text="0.684" /> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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24 <has_text text="0.376" /> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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25 </assert_contents> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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26 </output> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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27 </test> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
parents:
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28 </tests> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
parents:
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29 <help><![CDATA[ |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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30 BUM is the abbreviation for "Beta-Uniform Mixture (BUM) distribution." |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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31 |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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32 This tool (part of the package "Bionet") is used for fitting Beta-Uniform |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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33 mixture model to a P-value distribution, the output of which is two model |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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34 parameters: lambda and alpha, kept in a text file, the first line is |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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35 lambda; the second, alpha. |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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36 ]]></help> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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37 <citations> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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38 <citation type="doi">10.1093/bioinformatics/btq089</citation> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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39 <citation type="doi">10.1093/bioinformatics/btn161</citation> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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40 </citations> |
e41ec5af7472
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz commit b0b2c64a46bdd9beebdfb7fc5312f75346483763
iuc
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41 </tool> |