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comparison hyphy_sm19.xml @ 0:ae7c42d49717 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author iuc
date Wed, 21 Aug 2019 12:25:55 -0400
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-1:000000000000 0:ae7c42d49717
1 <?xml version="1.0"?>
2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="@VERSION@+galaxy0">
3 <description>Partition Tree using Modified Slatkin-Maddison Test</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_file' sm19_input.nhx &&
10 @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf ./sm19_input.nhx
11 #for $n, $partition in enumerate($partitions):
12 '${partition.label}'
13 '${partition.regex}'
14 #end for
15 $replicates
16 ]]></command>
17 <inputs>
18 <param name="input_file" type="data" format="nhx" label="Input tree"/>
19 <repeat name="partitions" min="2" max="50" title="Partitions">
20 <param name="label" type="text" label="Partition label"/>
21 <param name="regex" type="text" label="Regular expression">
22 <sanitizer>
23 <valid initial="string.printable">
24 <remove value="'"/>
25 </valid>
26 <mapping initial="none">
27 <add source="'" target="__sq__"/>
28 </mapping>
29 </sanitizer>
30 </param>
31 </repeat>
32 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
33 </inputs>
34 <outputs>
35 <data name="sm19_output" format="hyphy_results.json" from_work_dir="sm19_input.nhx.json"/>
36 </outputs>
37 <tests>
38 <test>
39 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
40 <param name="replicates" value="1000"/>
41 <repeat name="partitions">
42 <param name="label" value="Blood"/>
43 <param name="regex" value="B[0-9]+"/>
44 </repeat>
45 <repeat name="partitions">
46 <param name="label" value="Semen"/>
47 <param name="regex" value="S[0-9]+"/>
48 </repeat>
49 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
50 </test>
51 <test>
52 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
53 <param name="replicates" value="1000"/>
54 <repeat name="partitions">
55 <param name="label" value="Blood"/>
56 <param name="regex" value="B[0-9]+"/>
57 </repeat>
58 <repeat name="partitions">
59 <param name="label" value="Semen"/>
60 <param name="regex" value="S[0-9]+"/>
61 </repeat>
62 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
63 </test>
64 </tests>
65 <help><![CDATA[
66 This analysis implements canonical and modified versions of the Slatkin-Maddison
67 phylogeny based test for population segregation. The test estimates the minimum
68 number of migration events using maximum parsimony, and then evaluating whether
69 or not this number is lower than expected in a panmictic or unstructured
70 population using permutation tests.
71 ]]></help>
72 <expand macro="citations">
73 <citation type="bibtex">
74 @UNPUBLISHED{slatkin,
75 author = "Slatkin M, Maddison WP",
76 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
77 year = "1989",
78 note = "Genetics 123(3):603-613",
79 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
80 </citation>
81 </expand>
82 </tool>