Mercurial > repos > rdvelazquez > hyphy_gard

annotate hyphy_gard.xml @ 5:9640a5b51502 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 10:20:19 -0400
parents 876a69d2c6d7
children
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_gard" name="HyPhy-GARD" version="2.5.0+galaxy0">
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3 <description>: Recombination Detection</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 ln -s '$input_file' gard_input.fa &&
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10 @HYPHY_INVOCATION@ gard
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11 --alignment `pwd`/gard_input.fa
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12 --type
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13 --code
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14 --model
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15 --rv '$rate'
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16 --rate-classes '$rate_classes'
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17
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18 > '$gard_log' &&
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19 ]]></command>
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20 <inputs>
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21 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
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22 <conditional name="rate_cond">
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23 <param name="rate" type="select" label="Rate variation">
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24 <option value="None">None</option>
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25 <option value="GDD">General Discrete</option>
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26 <option value="Gamma">Beta-Gamma</option>
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27 </param>
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28 <when value="1"/>
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29 <when value="2">
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30 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
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31 </when>
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32 <when value="3">
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33 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
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34 </when>
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35 </conditional>
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36 </inputs>
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37 <outputs>
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38 <data name="gard_log" format="txt"/>
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39 <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/>
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40 <data name="translated" format="hyphy_json_results" from_work_dir="gard_input.fa.translated.json"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
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45 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 GARD (Genetic Algorithm for Recombination Detection) is a method to screen a multiple sequence analysis for the presence of recombination and is extremely useful as a pre-processing step for selection inference. Because recombinant sequences cannot be adequately described with a single phylogenetic history, selection inference on recombinant data often leads to a significant increase in false positives. GARD alleviates this concern by comprehensively screening an alignment for recombination breakpoints and inferring a unique phylogenetic history for each detected recombination block.
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50 ]]></help>
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51 <expand macro="citations">
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52 <citation type="doi">10.1093/molbev/msl051</citation>
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53 </expand>
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54 </tool>