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comparison hyphy_sm19.xml @ 1:789b15630f96 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 11:16:56 -0500
parents 6b94d16f8623
children f93eb6f0f46f
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0:6b94d16f8623 1:789b15630f96
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 Test</description> 3 <description>- Partition Tree using Modified Slatkin-Maddison
4 <macros> 4 Test</description>
5 <import>macros.xml</import> 5 <macros>
6 </macros> 6 <import>macros.xml</import>
7 <requirements> 7 </macros>
8 <requirement type="package" version="2.4.0">hyphy</requirement> 8 <expand macro="requirements">
9 </requirements> 9 <requirement type="package" version="2.4.0">hyphy</requirement>
10 <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command> 10 </expand>
11 <command detect_errors="exit_code"> 11 <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command>
12 <![CDATA[ 12 <command detect_errors="exit_code"><![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 ]]> 22 ]]></command>
23 </command> 23 <inputs>
24 <inputs> 24 <param name="input_file" type="data" format="nhx" label="Input tree"/>
25 <param name="input_file" type="data" format="nhx" label="Input tree" /> 25 <repeat name="partitions" min="2" max="50" title="Partitions">
26 <repeat name="partitions" min="2" max="50" title="Partitions"> 26 <param name="label" type="text" label="Partition label"/>
27 <param name="label" type="text" label="Partition label" /> 27 <param name="regex" type="text" label="Regular expression">
28 <param name="regex" type="text" label="Regular expression"> 28 <sanitizer>
29 <sanitizer> 29 <valid initial="string.printable">
30 <valid initial="string.printable"> 30 <remove value="'"/>
31 <remove value="&apos;" /> 31 </valid>
32 </valid> 32 <mapping initial="none">
33 <mapping initial="none"> 33 <add source="'" target="__sq__"/>
34 <add source="&apos;" target="__sq__" /> 34 </mapping>
35 </mapping> 35 </sanitizer>
36 </sanitizer> 36 </param>
37 </param> 37 </repeat>
38 </repeat> 38 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
39 <param name="replicates" type="integer" min="1" max="1000000" value="100" /> 39 </inputs>
40 </inputs> 40 <outputs>
41 <outputs> 41 <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json"/>
42 <data name="sm19_output" format="json" from_work_dir="sm19_input.nhx.json" /> 42 </outputs>
43 </outputs> 43 <tests>
44 <tests> 44 <test>
45 <test> 45 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
46 <param name="input_file" ftype="fasta" value="sm19-in1.nhx" /> 46 <param name="replicates" value="1000"/>
47 <param name="replicates" value="1000" /> 47 <repeat name="partitions">
48 <repeat name="partitions"> 48 <param name="label" value="Blood"/>
49 <param name="label" value="Blood" /> 49 <param name="regex" value="B[0-9]+"/>
50 <param name="regex" value="B[0-9]+"/> 50 </repeat>
51 </repeat> 51 <repeat name="partitions">
52 <repeat name="partitions"> 52 <param name="label" value="Semen"/>
53 <param name="label" value="Semen" /> 53 <param name="regex" value="S[0-9]+"/>
54 <param name="regex" value="S[0-9]+"/> 54 </repeat>
55 </repeat> 55 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
56 <output name="sm19_output" file="sm19-out1.json" compare="sim_size" /> 56 </test>
57 </test> 57 <test>
58 <test> 58 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
59 <param name="input_file" ftype="fasta" value="sm19-in2.nhx" /> 59 <param name="replicates" value="1000"/>
60 <param name="replicates" value="1000" /> 60 <repeat name="partitions">
61 <repeat name="partitions"> 61 <param name="label" value="Blood"/>
62 <param name="label" value="Blood" /> 62 <param name="regex" value="B[0-9]+"/>
63 <param name="regex" value="B[0-9]+"/> 63 </repeat>
64 </repeat> 64 <repeat name="partitions">
65 <repeat name="partitions"> 65 <param name="label" value="Semen"/>
66 <param name="label" value="Semen" /> 66 <param name="regex" value="S[0-9]+"/>
67 <param name="regex" value="S[0-9]+"/> 67 </repeat>
68 </repeat> 68 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
69 <output name="sm19_output" file="sm19-out2.json" compare="sim_size" /> 69 </test>
70 </test> 70 </tests>
71 </tests> 71 <help><![CDATA[
72 <help>
73 <![CDATA[
74 This analysis implements canonical and modified versions of the Slatkin-Maddison 72 This analysis implements canonical and modified versions of the Slatkin-Maddison
75 phylogeny based test for population segregation. The test estimates the minimum 73 phylogeny based test for population segregation. The test estimates the minimum
76 number of migration events using maximum parsimony, and then evaluating whether 74 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 75 or not this number is lower than expected in a panmictic or unstructured
78 population using permutation tests. 76 population using permutation tests.
79 ]]> 77 ]]></help>
80 </help> 78 <expand macro="citations">
81 <expand macro="citations"> 79 <citation type="bibtex">@UNPUBLISHED{slatkin, author = "Slatkin
82 <citation type="bibtex"> 80 M, Maddison WP", title = "A cladistic measure of gene flow
83 @UNPUBLISHED{slatkin, 81 inferred from the phylogenies of alleles", year = "1989", note
84 author = "Slatkin M, Maddison WP", 82 = "Genetics 123(3):603-613", url =
85 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles", 83 "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}</citation>
86 year = "1989", 84 </expand>
87 note = "Genetics 123(3):603-613",
88 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
89 </citation>
90 </expand>
91 </tool> 85 </tool>