Mercurial > repos > rdvelazquez > hyphy_meme

annotate hyphy_meme.xml @ 3:f84a42d3ef98 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
author rdvelazquez
date Fri, 07 Jun 2019 10:20:49 -0400
parents cffd8bd6e3ec
children
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="2.5.0+galaxy0">
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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>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 ln -s '$input_file' meme_input.fa &&
f84a42d3ef98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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11 ln -s '$input_nhx' meme_input.nhx &&
f84a42d3ef98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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12 @HYPHY_INVOCATION@ meme
f84a42d3ef98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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13 --alignment `pwd`/meme_input.fa
f84a42d3ef98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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14 --tree `pwd`/meme_input.nhx
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15 --code '$gencodeid'
f84a42d3ef98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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16 --branches '$branches'
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17 --pvalue '$p_value'
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18 > '$meme_log'
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19 ]]>
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20 </command>
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21 <inputs>
1
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22 <expand macro="inputs" />
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23 <expand macro="gencode" />
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24 <expand macro="branches" />
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25 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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26 </inputs>
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27 <outputs>
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28 <data name="meme_log" format="txt" />
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29 <data name="meme_output" format="hyphy_json_results" from_work_dir="meme_input.fa.MEME.json" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_file" ftype="fasta" value="meme-in1.fa" />
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34 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />
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35 <param name="branches" value="1" />
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36 <param name="p_value" value="0.1" />
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37 <output name="meme_output" file="meme-out1.json" compare="sim_size" />
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38 </test>
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39 </tests>
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40 <help>
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41 <![CDATA[
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42 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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43 ]]>
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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>