Mercurial > repos > rdvelazquez > hyphy_absrel

annotate hyphy_absrel.xml @ 2:d61d01c0af4c draft

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author rdvelazquez
date Mon, 19 Nov 2018 14:26:45 -0500
parents 9e8344d39fb7
children edf8263a39cb
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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="@VERSION@+galaxy0">
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3 <description>: adaptive Branch Site REL</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 <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 ln -s '$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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12 ln -s '$input_nhx' absrel_input.nhx &&
9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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13 echo $gencodeid > tool_params &&
9e8344d39fb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'242b3b04d9e05475977bc6def0dd5e5e9fe4380d\n'-dirty
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14 echo `pwd`/absrel_input.fa >> tool_params &&
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15 echo `pwd`/absrel_input.nhx >> tool_params &&
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16 echo '$branches' >> tool_params &&
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17 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf > '$absrel_log'
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18 ]]>
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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 <param name="input_nhx" type="data" format="nhx" label="Input newick file" />
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23 <param name="gencodeid" type="select" label="Genetic code">
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24 <option value="1">Universal code</option>
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25 <option value="2">Vertebrate mitochondrial DNA code</option>
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26 <option value="3">Yeast mitochondrial DNA code</option>
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27 <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option>
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28 <option value="5">Invertebrate mitochondrial DNA code</option>
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29 <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option>
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30 <option value="7">Echinoderm mitochondrial DNA code</option>
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31 <option value="8">Euplotid Nuclear code</option>
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32 <option value="9">Alternative Yeast Nuclear code</option>
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33 <option value="10">Ascidian mitochondrial DNA code</option>
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34 <option value="11">Flatworm mitochondrial DNA code</option>
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35 <option value="12">Blepharisma Nuclear code</option>
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36 </param>
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37 <param name="branches" type="select" label="Set of branches to test">
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38 <option value="1">All branches</option>
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39 <option value="2">Internal branches</option>
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40 <option value="3">Leaf branches</option>
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41 <option value="4">Unlabeled branches</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data name="absrel_log" format="txt" />
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46 <data name="absrel_output" format="json" from_work_dir="absrel_input.fa.ABSREL.json" />
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input_file" ftype="fasta" value="absrel-in1.fa" />
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51 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" />
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52 <output name="absrel_output" file="absrel-out1.json" compare="sim_size" />
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 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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58 ]]>
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59 </help>
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60 <expand macro="citations">
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61 <citation type="doi">10.1093/molbev/msv022</citation>
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62 </expand>
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63 </tool>