Mercurial > repos > rdvelazquez > hyphy_sm19
changeset 1:789b15630f96 draft
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 |
| files | hyphy_sm19.xml |
| diffstat | 1 files changed, 68 insertions(+), 74 deletions(-) [+] |
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--- a/hyphy_sm19.xml Tue Mar 05 20:14:43 2019 -0500 +++ b/hyphy_sm19.xml Wed Mar 06 11:16:56 2019 -0500 @@ -1,15 +1,15 @@ <?xml version="1.0"?> <tool id="hyphy_sm19" name="HyPhy-SM2019" version="2.4.0+galaxy0"> - <description>- Partition Tree using Modified Slatkin-Maddison Test</description> - <macros> - <import>macros.xml</import> - </macros> - <requirements> - <requirement type="package" version="2.4.0">hyphy</requirement> - </requirements> - <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command> - <command detect_errors="exit_code"> - <![CDATA[ + <description>- Partition Tree using Modified Slatkin-Maddison + Test</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.4.0">hyphy</requirement> + </expand> + <version_command><![CDATA[HYPHYMP < <(echo && echo) | head -n 1 | awk '{print $1}']]></version_command> + <command detect_errors="exit_code"><![CDATA[ #set $count = len($partitions) ln -s '$input_file' sm19_input.nhx && @HYPHY_ENVIRONMENT@ HYPHYMP LIBPATH=\$HYPHY_LIB @@ -19,73 +19,67 @@ '${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="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[ + ]]></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="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> + ]]></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>