Mercurial > repos > iuc > hyphy_absrel

annotate hyphy_absrel.xml @ 3:fb40b0928cad draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:44:41 -0500
parents de93e1fbdc31
children 181f5b9f139f
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419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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1 <?xml version="1.0"?>
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fb40b0928cad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1">
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419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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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>
419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_file' absrel_input.fa &&
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_nhx' absrel_input.nhx &&
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fb40b0928cad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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11 @HYPHYMPI@ absrel
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12 --alignment ./absrel_input.fa
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 --tree ./absrel_input.nhx
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14 --code '$gencodeid'
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 --branches '$branches'
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16 --output '$absrel_output'
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17 #if $log:
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18 > '$absrel_log'
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19 #end if
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20 ]]></command>
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419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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21 <inputs>
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22 <expand macro="inputs"/>
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23 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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24 <expand macro="gencode"/>
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25 <expand macro="branches"/>
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419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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26 </inputs>
419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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27 <outputs>
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28 <data name="absrel_log" format="txt">
419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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29 <filter>log</filter>
419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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30 </data>
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31 <data name="absrel_output" format="hyphy_results.json" />
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419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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32 </outputs>
419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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33 <tests>
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34 <test>
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35 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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36 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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37 <param name="log" value="false"/>
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38 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
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419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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39 </test>
419cd817299c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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40 </tests>
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41 <help><![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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44 See the online documentation_ for more information.
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45
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46 .. _documentation: http://hyphy.org/methods/selection-methods/#absrel
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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>