Mercurial > repos > rdvelazquez > hyphy_meme

annotate hyphy_meme.xml @ 1:cffd8bd6e3ec draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'0a555981fa0582d59012c76c01c466db490831ed\n'-dirty
author rdvelazquez
date Mon, 11 Feb 2019 14:31:06 -0500
parents 1fe6d55b5a9b
children f84a42d3ef98
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1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+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" />
1
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code">
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10 <![CDATA[
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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11 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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12 ln -s '$input_file' meme_input.fa &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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13 ln -s '$input_nhx' meme_input.nhx &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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14 echo $gencodeid > tool_params &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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15 echo `pwd`/meme_input.fa >> tool_params &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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16 echo `pwd`/meme_input.nhx >> tool_params &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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17 echo $branches >> tool_params &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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18 echo $p_value >> tool_params &&
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
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20 ]]>
1fe6d55b5a9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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21 </command>
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22 <inputs>
1
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23 <expand macro="inputs" />
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24 <expand macro="gencode" />
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25 <expand macro="branches" />
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26 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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27 </inputs>
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28 <outputs>
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29 <data name="meme_log" format="txt" />
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30 <data name="meme_output" format="hyphy_json_results" from_work_dir="meme_input.fa.MEME.json" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_file" ftype="fasta" value="meme-in1.fa" />
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35 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx" />
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36 <param name="branches" value="1" />
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37 <param name="p_value" value="0.1" />
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38 <output name="meme_output" file="meme-out1.json" compare="sim_size" />
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39 </test>
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40 </tests>
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41 <help>
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42 <![CDATA[
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43 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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44 ]]>
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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>