Mercurial > repos > iuc > hyphy_sm19

annotate hyphy_sm19.xml @ 0:30c8e7cc19df draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:18:31 -0400
parents
children a57d5219632c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 <?xml version="1.0"?>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="@VERSION@+galaxy0">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 <description>Partition Tree using Modified Slatkin-Maddison Test</description>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 <macros>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5 <import>macros.xml</import>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 </macros>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 <expand macro="requirements"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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8 <command detect_errors="exit_code"><![CDATA[
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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9 ln -s '$input_file' sm19_input.nhx &&
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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10 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf ./sm19_input.nhx
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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11 #for $n, $partition in enumerate($partitions):
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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12 '${partition.label}'
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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13 '${partition.regex}'
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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14 #end for
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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15 $replicates
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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16 ]]></command>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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17 <inputs>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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18 <param name="input_file" type="data" format="nhx" label="Input tree"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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19 <repeat name="partitions" min="2" max="50" title="Partitions">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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20 <param name="label" type="text" label="Partition label"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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21 <param name="regex" type="text" label="Regular expression">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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22 <sanitizer>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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23 <valid initial="string.printable">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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24 <remove value="'"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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25 </valid>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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26 <mapping initial="none">
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27 <add source="'" target="__sq__"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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28 </mapping>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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29 </sanitizer>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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30 </param>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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31 </repeat>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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32 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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33 </inputs>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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34 <outputs>
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35 <data name="sm19_output" format="hyphy_results.json" from_work_dir="sm19_input.nhx.json"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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36 </outputs>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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37 <tests>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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38 <test>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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39 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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40 <param name="replicates" value="1000"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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41 <repeat name="partitions">
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42 <param name="label" value="Blood"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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43 <param name="regex" value="B[0-9]+"/>
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44 </repeat>
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45 <repeat name="partitions">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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46 <param name="label" value="Semen"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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47 <param name="regex" value="S[0-9]+"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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48 </repeat>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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49 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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50 </test>
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51 <test>
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52 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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53 <param name="replicates" value="1000"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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54 <repeat name="partitions">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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55 <param name="label" value="Blood"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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56 <param name="regex" value="B[0-9]+"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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57 </repeat>
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58 <repeat name="partitions">
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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59 <param name="label" value="Semen"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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60 <param name="regex" value="S[0-9]+"/>
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61 </repeat>
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62 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 This analysis implements canonical and modified versions of the Slatkin-Maddison
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67 phylogeny based test for population segregation. The test estimates the minimum
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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68 number of migration events using maximum parsimony, and then evaluating whether
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69 or not this number is lower than expected in a panmictic or unstructured
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70 population using permutation tests.
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71 ]]></help>
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72 <expand macro="citations">
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73 <citation type="bibtex">
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74 @UNPUBLISHED{slatkin,
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75 author = "Slatkin M, Maddison WP",
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76 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
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77 year = "1989",
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78 note = "Genetics 123(3):603-613",
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79 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
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80 </citation>
30c8e7cc19df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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81 </expand>
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82 </tool>