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comparison 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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-1:000000000000 0:6b94d16f8623
1 <?xml version="1.0"?>
2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0">
3 <description>- Partition Tree using Modified Slatkin-Maddison Test</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="2.4.0">hyphy</requirement>
9 </requirements>
10 <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
11 <command detect_errors="exit_code">
12 <![CDATA[
13 #set $count = len($partitions)
14 ln -s '$input_file' sm19_input.nhx &&
15 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
16 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count
17 #for $n, $partition in enumerate($partitions):
18 '${partition.label}'
19 '${partition.regex}'
20 #end for
21 $replicates
22 ]]>
23 </command>
24 <inputs>
25 <param name="input_file" type="data" format="nhx" label="Input tree" />
26 <repeat name="partitions" min="2" max="50" title="Partitions">
27 <param name="label" type="text" label="Partition label" />
28 <param name="regex" type="text" label="Regular expression">
29 <sanitizer>
30 <valid initial="string.printable">
31 <remove value="&apos;" />
32 </valid>
33 <mapping initial="none">
34 <add source="&apos;" target="__sq__" />
35 </mapping>
36 </sanitizer>
37 </param>
38 </repeat>
39 <param name="replicates" type="integer" min="1" max="1000000" value="100" />
40 </inputs>
41 <outputs>
42 <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="input_file" ftype="fasta" value="sm19-in1.nhx" />
47 <param name="replicates" value="1000" />
48 <repeat name="partitions">
49 <param name="label" value="Blood" />
50 <param name="regex" value="B[0-9]+"/>
51 </repeat>
52 <repeat name="partitions">
53 <param name="label" value="Semen" />
54 <param name="regex" value="S[0-9]+"/>
55 </repeat>
56 <output name="sm19_output" file="sm19-out1.json" compare="sim_size" />
57 </test>
58 <test>
59 <param name="input_file" ftype="fasta" value="sm19-in2.nhx" />
60 <param name="replicates" value="1000" />
61 <repeat name="partitions">
62 <param name="label" value="Blood" />
63 <param name="regex" value="B[0-9]+"/>
64 </repeat>
65 <repeat name="partitions">
66 <param name="label" value="Semen" />
67 <param name="regex" value="S[0-9]+"/>
68 </repeat>
69 <output name="sm19_output" file="sm19-out2.json" compare="sim_size" />
70 </test>
71 </tests>
72 <help>
73 <![CDATA[
74 This analysis implements canonical and modified versions of the Slatkin-Maddison
75 phylogeny based test for population segregation. The test estimates the minimum
76 number of migration events using maximum parsimony, and then evaluating whether
77 or not this number is lower than expected in a panmictic or unstructured
78 population using permutation tests.
79 ]]>
80 </help>
81 <expand macro="citations">
82 <citation type="bibtex">
83 @UNPUBLISHED{slatkin,
84 author = "Slatkin M, Maddison WP",
85 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
86 year = "1989",
87 note = "Genetics 123(3):603-613",
88 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
89 </citation>
90 </expand>
91 </tool>