Mercurial > repos > stephenshank > hyphy_absrel

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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 14:29:44 -0500
parents 32b1229ad002
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daec257d4976 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"?>
daec257d4976 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_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
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3 <description>adaptive Branch Site Random Effects Likelihood</description>
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4 <macros>
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5 <import>macros.xml</import>
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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6 </macros>
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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">
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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10 <![CDATA[
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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11 ln -s '$input_file' absrel_input.fa &&
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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12 ln -s '$input_nhx' absrel_input.nhx &&
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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13 echo $gencodeid > tool_params &&
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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14 echo `pwd`/absrel_input.fa >> tool_params &&
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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15 echo `pwd`/absrel_input.nhx >> tool_params &&
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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16 echo '$branches' >> tool_params &&
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17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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18 #if $log:
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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19 > '$absrel_log'
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20 #end if
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daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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21 ]]>
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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22 </command>
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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23 <inputs>
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24 <expand macro="inputs" />
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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25 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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26 <expand macro="gencode" />
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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27 <expand macro="branches" />
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28 </inputs>
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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29 <outputs>
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30 <data name="absrel_log" format="txt">
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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31 <filter>log</filter>
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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32 </data>
32b1229ad002 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f937b10585fe4b760772a6f1a7af20b428be9878-dirty
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33 <data name="absrel_output" format="hyphy_json_results" from_work_dir="absrel_input.fa.ABSREL.json" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
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38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
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39 <param name="log" value="false" />
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40 <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
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41 </test>
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42 </tests>
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43 <help>
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44 <![CDATA[
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45 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
daec257d4976 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 242b3b04d9e05475977bc6def0dd5e5e9fe4380d-dirty
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46 ]]>
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47 </help>
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48 <expand macro="citations">
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49 <citation type="doi">10.1093/molbev/msv022</citation>
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50 </expand>
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51 </tool>