annotate hyphy_meme.xml @ 1:d02c8e6f7f2a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
author iuc
date Thu, 13 Feb 2020 15:03:27 -0500
parents 7b3f9c78cf6d
children b15d64d85c03
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7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 <description>Mixed Effects Model of Evolution</description>
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4 <macros>
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5 <import>macros.xml</import>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_file' meme_input.fa &&
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_nhx' meme_input.nhx &&
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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11 @HYPHY_INVOCATION@ meme
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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12 --alignment ./meme_input.fa
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13 --tree ./meme_input.nhx
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 --code '$gencodeid'
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15 --branches '$branches'
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16 --pvalue '$p_value'
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17 > '$meme_log'
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18 ]]></command>
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19 <inputs>
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20 <expand macro="inputs"/>
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21 <expand macro="gencode"/>
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22 <expand macro="branches"/>
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23 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
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24 </inputs>
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25 <outputs>
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26 <data name="meme_log" format="txt"/>
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27 <data name="meme_output" format="hyphy_results.json" from_work_dir="meme_input.fa.MEME.json"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
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32 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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33 <param name="branches" value="All"/>
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34 <param name="p_value" value="0.1"/>
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35 <output name="meme_output" file="meme-out1.json" compare="sim_size"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches.
1
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40
d02c8e6f7f2a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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41 See the online documentation_ for more information.
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42
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43 .. _documentation: http://hyphy.org/methods/selection-methods/#meme
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44 ]]></help>
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45 <expand macro="citations">
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46 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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47 </expand>
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48 </tool>