Mercurial > repos > rdvelazquez > hyphy_sm19

annotate hyphy_sm19.xml @ 0:6b94d16f8623 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 Tue, 05 Mar 2019 20:14:43 -0500
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children 789b15630f96
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6b94d16f8623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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1 <?xml version="1.0"?>
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2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0">
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3 <description>- Partition Tree using Modified Slatkin-Maddison Test</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 <requirements>
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8 <requirement type="package" version="2.4.0">hyphy</requirement>
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9 </requirements>
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10 <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 #set $count = len($partitions)
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14 ln -s '$input_file' sm19_input.nhx &&
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15 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
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16 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count
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17 #for $n, $partition in enumerate($partitions):
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18 '${partition.label}'
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19 '${partition.regex}'
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20 #end for
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21 $replicates
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param name="input_file" type="data" format="nhx" label="Input tree" />
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26 <repeat name="partitions" min="2" max="50" title="Partitions">
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27 <param name="label" type="text" label="Partition label" />
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28 <param name="regex" type="text" label="Regular expression">
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29 <sanitizer>
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30 <valid initial="string.printable">
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31 <remove value="&apos;" />
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32 </valid>
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33 <mapping initial="none">
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34 <add source="&apos;" target="__sq__" />
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35 </mapping>
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36 </sanitizer>
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37 </param>
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38 </repeat>
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39 <param name="replicates" type="integer" min="1" max="1000000" value="100" />
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40 </inputs>
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41 <outputs>
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42 <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input_file" ftype="fasta" value="sm19-in1.nhx" />
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47 <param name="replicates" value="1000" />
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48 <repeat name="partitions">
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49 <param name="label" value="Blood" />
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50 <param name="regex" value="B[0-9]+"/>
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51 </repeat>
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52 <repeat name="partitions">
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53 <param name="label" value="Semen" />
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54 <param name="regex" value="S[0-9]+"/>
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55 </repeat>
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56 <output name="sm19_output" file="sm19-out1.json" compare="sim_size" />
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57 </test>
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58 <test>
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59 <param name="input_file" ftype="fasta" value="sm19-in2.nhx" />
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60 <param name="replicates" value="1000" />
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61 <repeat name="partitions">
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62 <param name="label" value="Blood" />
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63 <param name="regex" value="B[0-9]+"/>
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64 </repeat>
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65 <repeat name="partitions">
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66 <param name="label" value="Semen" />
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67 <param name="regex" value="S[0-9]+"/>
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68 </repeat>
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69 <output name="sm19_output" file="sm19-out2.json" compare="sim_size" />
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74 This analysis implements canonical and modified versions of the Slatkin-Maddison
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75 phylogeny based test for population segregation. The test estimates the minimum
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76 number of migration events using maximum parsimony, and then evaluating whether
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77 or not this number is lower than expected in a panmictic or unstructured
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78 population using permutation tests.
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79 ]]>
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80 </help>
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81 <expand macro="citations">
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82 <citation type="bibtex">
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83 @UNPUBLISHED{slatkin,
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84 author = "Slatkin M, Maddison WP",
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85 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
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86 year = "1989",
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87 note = "Genetics 123(3):603-613",
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88 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
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89 </citation>
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90 </expand>
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91 </tool>