Mercurial > repos > iuc > hyphy_busted

annotate hyphy_busted.xml @ 3:4c8ccfe4a003 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 21:36:54 +0000
parents 1d41fc8c04d7
children a0eaa84a5cf8
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3e7799d80897 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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4c8ccfe4a003 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
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2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1">
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3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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4 <macros>
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5 <import>macros.xml</import>
3e7799d80897 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 '$input_file' busted_input.fa &&
d568d72737a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 ln -s '$input_nhx' busted_input.nhx &&
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11 hyphy busted
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12 --alignment ./busted_input.fa
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13 --tree ./busted_input.nhx
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14 --code $gencodeid
d568d72737a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 --branches '$branches'
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16 --output '$busted_output'
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17 > '$busted_log'
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18 ]]></command>
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3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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19 <inputs>
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20 <expand macro="inputs"/>
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21 <expand macro="gencode"/>
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22 <expand macro="branches"/>
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23 </inputs>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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24 <outputs>
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25 <data name="busted_log" format="txt"/>
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26 <data name="busted_output" format="hyphy_results.json" />
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3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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27 </outputs>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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28 <tests>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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29 <test>
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30 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
d568d72737a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
d568d72737a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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32 <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
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3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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33 </test>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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34 </tests>
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35 <help><![CDATA[
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36 BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection.
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1d41fc8c04d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
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38 See the online documentation_ for more information.
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39
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40 .. _documentation: http://hyphy.org/methods/selection-methods/#busted
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41 ]]></help>
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42 <expand macro="citations">
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43 <citation type="doi">10.1093/molbev/msv035</citation>
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44 </expand>
3e7799d80897 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
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45 </tool>