Mercurial > repos > iuc > hyphy_sm19
view hyphy_sm19.xml @ 2:3a04bc15a251 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author | iuc |
---|---|
date | Fri, 14 Feb 2020 16:46:23 -0500 |
parents | ae7c42d49717 |
children | 5f1830cb9135 |
line wrap: on
line source
<?xml version="1.0"?> <tool id="hyphy_sm19" name="HyPhy-SM2019" version="@VERSION@+galaxy0"> <description>Partition Tree using Modified Slatkin-Maddison Test</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input_file' sm19_input.nhx && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SM-2019.bf ./sm19_input.nhx #for $n, $partition in enumerate($partitions): '${partition.label}' '${partition.regex}' #end for $replicates ]]></command> <inputs> <param name="input_file" type="data" format="nhx" label="Input tree"/> <repeat name="partitions" min="2" max="50" title="Partitions"> <param name="label" type="text" label="Partition label"/> <param name="regex" type="text" label="Regular expression"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </repeat> <param name="replicates" type="integer" min="1" max="1000000" value="100"/> </inputs> <outputs> <data name="sm19_output" format="hyphy_results.json" from_work_dir="sm19_input.nhx.json"/> </outputs> <tests> <test> <param name="input_file" ftype="fasta" value="sm19-in1.nhx"/> <param name="replicates" value="1000"/> <repeat name="partitions"> <param name="label" value="Blood"/> <param name="regex" value="B[0-9]+"/> </repeat> <repeat name="partitions"> <param name="label" value="Semen"/> <param name="regex" value="S[0-9]+"/> </repeat> <output name="sm19_output" file="sm19-out1.json" compare="sim_size"/> </test> <test> <param name="input_file" ftype="fasta" value="sm19-in2.nhx"/> <param name="replicates" value="1000"/> <repeat name="partitions"> <param name="label" value="Blood"/> <param name="regex" value="B[0-9]+"/> </repeat> <repeat name="partitions"> <param name="label" value="Semen"/> <param name="regex" value="S[0-9]+"/> </repeat> <output name="sm19_output" file="sm19-out2.json" compare="sim_size"/> </test> </tests> <help><![CDATA[ This analysis implements canonical and modified versions of the Slatkin-Maddison phylogeny based test for population segregation. The test estimates the minimum number of migration events using maximum parsimony, and then evaluating whether or not this number is lower than expected in a panmictic or unstructured population using permutation tests. ]]></help> <expand macro="citations"> <citation type="bibtex"> @UNPUBLISHED{slatkin, author = "Slatkin M, Maddison WP", title = "A cladistic measure of gene flow inferred from the phylogenies of alleles", year = "1989", note = "Genetics 123(3):603-613", url = "https://www.ncbi.nlm.nih.gov/pubmed/2599370"} </citation> </expand> </tool>