Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 2:b15d64d85c03 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:46:45 -0500
parents d02c8e6f7f2a
children 33040ebb30c6
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1 <?xml version="1.0"?>
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b15d64d85c03 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1">
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3 <description>Mixed Effects Model of Evolution</description>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 <macros>
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5 <import>macros.xml</import>
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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 '$input_file' meme_input.fa &&
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10 ln -s '$input_nhx' meme_input.nhx &&
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b15d64d85c03 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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11 @HYPHYMPI@ meme
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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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12 --alignment ./meme_input.fa
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 --tree ./meme_input.nhx
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14 --code '$gencodeid'
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 --branches '$branches'
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16 --pvalue '$p_value'
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17 --output '$meme_output'
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18 > '$meme_log'
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19 ]]></command>
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20 <inputs>
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21 <expand macro="inputs"/>
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22 <expand macro="gencode"/>
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23 <expand macro="branches"/>
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24 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 </inputs>
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26 <outputs>
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27 <data name="meme_log" format="txt"/>
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28 <data name="meme_output" format="hyphy_results.json" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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33 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
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34 <param name="branches" value="All"/>
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35 <param name="p_value" value="0.1"/>
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36 <output name="meme_output" file="meme-out1.json" compare="sim_size"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 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.
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41
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42 See the online documentation_ for more information.
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43
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44 .. _documentation: http://hyphy.org/methods/selection-methods/#meme
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45 ]]></help>
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46 <expand macro="citations">
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47 <citation type="doi">10.1371/journal.pgen.1002764</citation>
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48 </expand>
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49 </tool>