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comparison hyphy_sm19.xml @ 2:f93eb6f0f46f 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 Wed, 06 Mar 2019 13:21:59 -0500
parents 789b15630f96
children e2e7e6a88b0f
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1:789b15630f96 2:f93eb6f0f46f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0"> 2 <tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0">
3 <description>- Partition Tree using Modified Slatkin-Maddison 3 <description>- Partition Tree using Modified Slatkin-Maddison Test</description>
4 Test</description> 4 <macros>
5 <macros> 5 <import>macros.xml</import>
6 <import>macros.xml</import> 6 </macros>
7 </macros> 7 <requirements>
8 <expand macro="requirements"> 8 <requirement type="package" version="2.4.0">hyphy</requirement>
9 <requirement type="package" version="2.4.0">hyphy</requirement> 9 </requirements>
10 </expand> 10 <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
11 <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command> 11 <command detect_errors="exit_code">
12 <command detect_errors="exit_code"><![CDATA[ 12 <![CDATA[
13 #set $count = len($partitions) 13 #set $count = len($partitions)
14 ln -s '$input_file' sm19_input.nhx && 14 ln -s '$input_file' sm19_input.nhx &&
15 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB 15 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
16 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count 16 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count
17 #for $n, $partition in enumerate($partitions): 17 #for $n, $partition in enumerate($partitions):
18 '${partition.label}' 18 '${partition.label}'
19 '${partition.regex}' 19 '${partition.regex}'
20 #end for 20 #end for
21 $replicates 21 $replicates
22 ]]></command> 22 ]]>
23 <inputs> 23 </command>
24 <param name="input_file" type="data" format="nhx" label="Input tree"/> 24 <inputs>
25 <repeat name="partitions" min="2" max="50" title="Partitions"> 25 <param name="input_file" type="data" format="nhx" label="Input tree" />
26 <param name="label" type="text" label="Partition label"/> 26 <repeat name="partitions" min="2" max="50" title="Partitions">
27 <param name="regex" type="text" label="Regular expression"> 27 <param name="label" type="text" label="Partition label" />
28 <sanitizer> 28 <param name="regex" type="text" label="Regular expression">
29 <valid initial="string.printable"> 29 <sanitizer>
30 <remove value="'"/> 30 <valid initial="string.printable">
31 </valid> 31 <remove value="&apos;" />
32 <mapping initial="none"> 32 </valid>
33 <add source="'" target="__sq__"/> 33 <mapping initial="none">
34 </mapping> 34 <add source="&apos;" target="__sq__" />
35 </sanitizer> 35 </mapping>
36 </param> 36 </sanitizer>
37 </repeat> 37 </param>
38 <param name="replicates" type="integer" min="1" max="1000000" value="100"/> 38 </repeat>
39 </inputs> 39 <param name="replicates" type="integer" min="1" max="1000000" value="100" />
40 <outputs> 40 </inputs>
41 <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json"/> 41 <outputs>
42 </outputs> 42 <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json" />
43 <tests> 43 </outputs>
44 <test> 44 <tests>
45 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/> 45 <test>
46 <param name="replicates" value="1000"/> 46 <param name="input_file" ftype="fasta" value="sm19-in1.nhx" />
47 <repeat name="partitions"> 47 <param name="replicates" value="1000" />
48 <param name="label" value="Blood"/> 48 <repeat name="partitions">
49 <param name="regex" value="B[0-9]+"/> 49 <param name="label" value="Blood" />
50 </repeat> 50 <param name="regex" value="B[0-9]+"/>
51 <repeat name="partitions"> 51 </repeat>
52 <param name="label" value="Semen"/> 52 <repeat name="partitions">
53 <param name="regex" value="S[0-9]+"/> 53 <param name="label" value="Semen" />
54 </repeat> 54 <param name="regex" value="S[0-9]+"/>
55 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/> 55 </repeat>
56 </test> 56 <output name="sm19_output" file="sm19-out1.json" compare="sim_size" />
57 <test> 57 </test>
58 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/> 58 <test>
59 <param name="replicates" value="1000"/> 59 <param name="input_file" ftype="fasta" value="sm19-in2.nhx" />
60 <repeat name="partitions"> 60 <param name="replicates" value="1000" />
61 <param name="label" value="Blood"/> 61 <repeat name="partitions">
62 <param name="regex" value="B[0-9]+"/> 62 <param name="label" value="Blood" />
63 </repeat> 63 <param name="regex" value="B[0-9]+"/>
64 <repeat name="partitions"> 64 </repeat>
65 <param name="label" value="Semen"/> 65 <repeat name="partitions">
66 <param name="regex" value="S[0-9]+"/> 66 <param name="label" value="Semen" />
67 </repeat> 67 <param name="regex" value="S[0-9]+"/>
68 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/> 68 </repeat>
69 </test> 69 <output name="sm19_output" file="sm19-out2.json" compare="sim_size" />
70 </tests> 70 </test>
71 <help><![CDATA[ 71 </tests>
72 <help>
73 <![CDATA[
72 This analysis implements canonical and modified versions of the Slatkin-Maddison 74 This analysis implements canonical and modified versions of the Slatkin-Maddison
73 phylogeny based test for population segregation. The test estimates the minimum 75 phylogeny based test for population segregation. The test estimates the minimum
74 number of migration events using maximum parsimony, and then evaluating whether 76 number of migration events using maximum parsimony, and then evaluating whether
75 or not this number is lower than expected in a panmictic or unstructured 77 or not this number is lower than expected in a panmictic or unstructured
76 population using permutation tests. 78 population using permutation tests.
77 ]]></help> 79 ]]>
78 <expand macro="citations"> 80 </help>
79 <citation type="bibtex">@UNPUBLISHED{slatkin, author = "Slatkin 81 <expand macro="citations">
80 M, Maddison WP", title = "A cladistic measure of gene flow 82 <citation type="bibtex">
81 inferred from the phylogenies of alleles", year = "1989", note 83 @UNPUBLISHED{slatkin,
82 = "Genetics 123(3):603-613", url = 84 author = "Slatkin M, Maddison WP",
83 "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}</citation> 85 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
84 </expand> 86 year = "1989",
87 note = "Genetics 123(3):603-613",
88 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
89 </citation>
90 </expand>
85 </tool> 91 </tool>