Mercurial > repos > rdvelazquez > hyphy_absrel

annotate hyphy_absrel.xml @ 13:35c1c523ae44 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 10:17:13 -0400
parents edf8263a39cb
children
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9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="2.5.0+galaxy0">
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3 <description>absrel</description>
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4 <macros>
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5 <import>macros.xml</import>
9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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9 <![CDATA[
9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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10 ln -s '$input_file' absrel_input.fa &&
9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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11 ln -s '$input_nhx' absrel_input.nhx &&
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12 @HYPHY_INVOCATION@ absrel
35c1c523ae44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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13 --alignment `pwd`/absrel_input.fa
35c1c523ae44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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14 --tree `pwd/absrel_input.nhx
35c1c523ae44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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15 --code '$gencodeid'
35c1c523ae44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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16 --branches '$branches'
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17 > '$absrel_log'
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18 ]]>
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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 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history" />
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23 <expand macro="gencode" />
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24 <expand macro="branches" />
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25 </inputs>
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26 <outputs>
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27 <data name="absrel_log" format="txt">
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28 <filter>log</filter>
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29 </data>
edf8263a39cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'446f1cfedd192ab0e7456495383c2099331379cc\n'-dirty
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30 <data name="absrel_output" format="hyphy_json_results" from_work_dir="absrel_input.fa.ABSREL.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="absrel-in1.fa" />
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35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
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36 <param name="log" value="false" />
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37 <output name="absrel_output" file="absrel-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 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.
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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">10.1093/molbev/msv022</citation>
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47 </expand>
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48 </tool>