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comparison 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
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3:e2e7e6a88b0f 4:65816621ff9f
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="2.5.0+galaxy0">
3 <description>- Partition Tree using Modified Slatkin-Maddison Test</description> 3 <description>- Partition Tree using Modified Slatkin-Maddison Test</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <expand macro="requirements"/>
8 <requirement type="package" version="2.4.0">hyphy</requirement> 8 <command detect_errors="exit_code"><![CDATA[
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) 9 #set $count = len($partitions)
14 ln -s '$input_file' sm19_input.nhx && 10 ln -s '$input_file' sm19_input.nhx &&
15 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB 11 @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB
16 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count 12 \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf `pwd`/sm19_input.nhx $count
17 #for $n, $partition in enumerate($partitions): 13 #for $n, $partition in enumerate($partitions):
18 '${partition.label}' 14 '${partition.label}'
19 '${partition.regex}' 15 '${partition.regex}'
20 #end for 16 #end for
21 $replicates 17 $replicates
22 ]]> 18 ]]></command>
23 </command> 19 <inputs>
24 <inputs> 20 <param name="input_file" type="data" format="nhx" label="Input tree"/>
25 <param name="input_file" type="data" format="nhx" label="Input tree" /> 21 <repeat name="partitions" min="2" max="50" title="Partitions">
26 <repeat name="partitions" min="2" max="50" title="Partitions"> 22 <param name="label" type="text" label="Partition label"/>
27 <param name="label" type="text" label="Partition label" /> 23 <param name="regex" type="text" label="Regular expression">
28 <param name="regex" type="text" label="Regular expression"> 24 <sanitizer>
29 <sanitizer> 25 <valid initial="string.printable">
30 <valid initial="string.printable"> 26 <remove value="'"/>
31 <remove value="&apos;" /> 27 </valid>
32 </valid> 28 <mapping initial="none">
33 <mapping initial="none"> 29 <add source="'" target="__sq__"/>
34 <add source="&apos;" target="__sq__" /> 30 </mapping>
35 </mapping> 31 </sanitizer>
36 </sanitizer> 32 </param>
37 </param> 33 </repeat>
38 </repeat> 34 <param name="replicates" type="integer" min="1" max="1000000" value="100"/>
39 <param name="replicates" type="integer" min="1" max="1000000" value="100" /> 35 </inputs>
40 </inputs> 36 <outputs>
41 <outputs> 37 <data name="sm19_output" format="hyphy_json_results" from_work_dir="sm19_input.nhx.json"/>
42 <data name="sm19_output" format="hyphy_json_results" from_work_dir="sm19_input.nhx.json" /> 38 </outputs>
43 </outputs> 39 <tests>
44 <tests> 40 <test>
45 <test> 41 <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/>
46 <param name="input_file" ftype="fasta" value="sm19-in1.nhx" /> 42 <param name="replicates" value="1000"/>
47 <param name="replicates" value="1000" /> 43 <repeat name="partitions">
48 <repeat name="partitions"> 44 <param name="label" value="Blood"/>
49 <param name="label" value="Blood" /> 45 <param name="regex" value="B[0-9]+"/>
50 <param name="regex" value="B[0-9]+"/> 46 </repeat>
51 </repeat> 47 <repeat name="partitions">
52 <repeat name="partitions"> 48 <param name="label" value="Semen"/>
53 <param name="label" value="Semen" /> 49 <param name="regex" value="S[0-9]+"/>
54 <param name="regex" value="S[0-9]+"/> 50 </repeat>
55 </repeat> 51 <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/>
56 <output name="sm19_output" file="sm19-out1.json" compare="sim_size" /> 52 </test>
57 </test> 53 <test>
58 <test> 54 <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/>
59 <param name="input_file" ftype="fasta" value="sm19-in2.nhx" /> 55 <param name="replicates" value="1000"/>
60 <param name="replicates" value="1000" /> 56 <repeat name="partitions">
61 <repeat name="partitions"> 57 <param name="label" value="Blood"/>
62 <param name="label" value="Blood" /> 58 <param name="regex" value="B[0-9]+"/>
63 <param name="regex" value="B[0-9]+"/> 59 </repeat>
64 </repeat> 60 <repeat name="partitions">
65 <repeat name="partitions"> 61 <param name="label" value="Semen"/>
66 <param name="label" value="Semen" /> 62 <param name="regex" value="S[0-9]+"/>
67 <param name="regex" value="S[0-9]+"/> 63 </repeat>
68 </repeat> 64 <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/>
69 <output name="sm19_output" file="sm19-out2.json" compare="sim_size" /> 65 </test>
70 </test> 66 </tests>
71 </tests> 67 <help><![CDATA[
72 <help>
73 <![CDATA[
74 This analysis implements canonical and modified versions of the Slatkin-Maddison 68 This analysis implements canonical and modified versions of the Slatkin-Maddison
75 phylogeny based test for population segregation. The test estimates the minimum 69 phylogeny based test for population segregation. The test estimates the minimum
76 number of migration events using maximum parsimony, and then evaluating whether 70 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 71 or not this number is lower than expected in a panmictic or unstructured
78 population using permutation tests. 72 population using permutation tests.
79 ]]> 73 ]]></help>
80 </help> 74 <expand macro="citations">
81 <expand macro="citations"> 75 <citation type="bibtex">
82 <citation type="bibtex">
83 @UNPUBLISHED{slatkin, 76 @UNPUBLISHED{slatkin,
84 author = "Slatkin M, Maddison WP", 77 author = "Slatkin M, Maddison WP",
85 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles", 78 title = "A cladistic measure of gene flow inferred from the phylogenies of alleles",
86 year = "1989", 79 year = "1989",
87 note = "Genetics 123(3):603-613", 80 note = "Genetics 123(3):603-613",
88 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"} 81 url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"}
89 </citation> 82 </citation>
90 </expand> 83 </expand>
91 </tool> 84 </tool>