Mercurial > repos > stephenshank > hyphy_meme

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty
author stephenshank
date Wed, 06 Mar 2019 14:31:33 -0500
parents e44501a5cdcc
children
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1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
stephenshank
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1 <?xml version="1.0"?>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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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>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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6 </macros>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code">
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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10 <![CDATA[
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11 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-1} &&
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1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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12 ln -s '$input_file' meme_input.fa &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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13 ln -s '$input_nhx' meme_input.nhx &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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14 echo $gencodeid > tool_params &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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15 echo `pwd`/meme_input.fa >> tool_params &&
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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16 echo `pwd`/meme_input.nhx >> tool_params &&
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17 echo $branches >> tool_params &&
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18 echo $p_value >> tool_params &&
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19 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/MEME.bf > '$meme_log'
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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20 ]]>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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21 </command>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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22 <inputs>
3
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23 <expand macro="inputs" />
3b7f2dbb5c44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty
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24 <expand macro="gencode" />
3b7f2dbb5c44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6e7f074d80e0f35516e223b76e73f019ad45dd74-dirty
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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" />
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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27 </inputs>
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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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" />
1a72da7a000d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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39 </test>
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40 </tests>
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41 <help>
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42 <![CDATA[
2
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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>