Mercurial > repos > rdvelazquez > hyphy_gard

annotate hyphy_gard.xml @ 2:9e533457ebc0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
author rdvelazquez
date Mon, 18 Feb 2019 15:12:22 -0500
parents e489b7f00db7
children 107a4340acb0
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+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 <expand macro="requirements">
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8 <requirement type="package" version="1.0.4">translate-gard</requirement>
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9 </expand>
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10 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 export MPI_NODE_COUNT=\${GALAXY_SLOTS:-2} &&
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13 ln -s '$input_file' gard_input.fa &&
e489b7f00db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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14 echo `pwd`/gard_input.fa > tool_params &&
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15 echo "010010" >> tool_params &&
e489b7f00db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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16 echo $rate_cond.rate >> tool_params &&
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17 #if str($rate_cond.rate) != "1":
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18 echo $rate_cond.rate_classes >> tool_params &&
e489b7f00db7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6da8a2296bb256e47852690cf2221a7c943d8adc\n'-dirty
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19 #end if
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20 echo `pwd`/"gard_input.GARD" >> tool_params &&
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21 @HYPHYMPI_INVOCATION@ \$HYPHYMPI_LIB/TemplateBatchFiles/GARD.bf > '$gard_log' &&
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22 translate-gard -i gard_input.GARD -j gard_input.GARD.json -o gard_input.fa.translated.json
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23 ]]></command>
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24 <inputs>
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25 <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
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26 <conditional name="rate_cond">
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27 <param name="rate" type="select" label="Rate variation">
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28 <option value="1">None</option>
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29 <option value="2">General Discrete</option>
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30 <option value="3">Beta-Gamma</option>
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31 </param>
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32 <when value="1"/>
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33 <when value="2">
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34 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
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35 </when>
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36 <when value="3">
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37 <param name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes"/>
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data name="gard_log" format="txt"/>
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43 <data name="gard_output" format="nex" from_work_dir="gard_input.GARD_finalout"/>
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44 <data name="translated" format="hyphy_json_results" from_work_dir="gard_input.fa.translated.json"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
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49 <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 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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54 ]]></help>
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55 <expand macro="citations">
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56 <citation type="doi">10.1093/molbev/msl051</citation>
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57 </expand>
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58 </tool>