Mercurial > repos > rdvelazquez > hyphy_sm19

annotate hyphy_sm19.xml @ 4:65816621ff9f 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 10:22:23 -0400
parents e2e7e6a88b0f
children
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1 <?xml version="1.0"?>
4
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2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.5.0+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 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
0
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9 #set $count = len($partitions)
6b94d16f8623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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10 ln -s '$input_file' sm19_input.nhx &&
6b94d16f8623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty
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11 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
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12 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count
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13 #for $n, $partition in enumerate($partitions):
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14 '${partition.label}'
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15 '${partition.regex}'
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16 #end for
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17 $replicates
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18 ]]></command>
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19 <inputs>
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20 <param name="input_file" type="data" format="nhx" label="Input tree"/>
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21 <repeat name="partitions" min="2" max="50" title="Partitions">
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22 <param name="label" type="text" label="Partition label"/>
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23 <param name="regex" type="text" label="Regular expression">
65816621ff9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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24 <sanitizer>
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25 <valid initial="string.printable">
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26 <remove value="'"/>
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27 </valid>
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28 <mapping initial="none">
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29 <add source="'" target="__sq__"/>
65816621ff9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6c73b2e4c05bdddaef2026feb1073c1b0b4aa12e-dirty
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30 </mapping>
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31 </sanitizer>
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32 </param>
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33 </repeat>
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34 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
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35 </inputs>
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36 <outputs>
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37 <data name="sm19_output" format="hyphy_json_results" from_work_dir="sm19_input.nhx.json"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
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42 <param name="replicates" value="1000"/>
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43 <repeat name="partitions">
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44 <param name="label" value="Blood"/>
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45 <param name="regex" value="B[0-9]+"/>
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46 </repeat>
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47 <repeat name="partitions">
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48 <param name="label" value="Semen"/>
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49 <param name="regex" value="S[0-9]+"/>
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50 </repeat>
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51 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
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52 </test>
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53 <test>
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54 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
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55 <param name="replicates" value="1000"/>
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56 <repeat name="partitions">
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57 <param name="label" value="Blood"/>
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58 <param name="regex" value="B[0-9]+"/>
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59 </repeat>
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60 <repeat name="partitions">
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61 <param name="label" value="Semen"/>
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62 <param name="regex" value="S[0-9]+"/>
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63 </repeat>
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64 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
0
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68 This analysis implements canonical and modified versions of the Slatkin-Maddison
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69 phylogeny based test for population segregation. The test estimates the minimum
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70 number of migration events using maximum parsimony, and then evaluating whether
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71 or not this number is lower than expected in a panmictic or unstructured
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72 population using permutation tests.
4
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73 ]]></help>
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74 <expand macro="citations">
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75 <citation type="bibtex">
2
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76 @UNPUBLISHED{slatkin,
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77 author = "Slatkin M, Maddison WP",
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78 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
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79 year = "1989",
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80 note = "Genetics 123(3):603-613",
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81 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
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82 </citation>
4
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83 </expand>
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84 </tool>