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Update indentation to IUC preference.
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Fix a few errors in wrappers, correct test data.
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@davebx
davebx committed Aug 14, 2019
1 parent 70cacf6 commit 0c7efad
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Showing 16 changed files with 11,476 additions and 10,808 deletions.
80 changes: 40 additions & 40 deletions tools/hyphy/hyphy_absrel.xml
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Original file line number Diff line number Diff line change
@@ -1,44 +1,44 @@
<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="2.5.0+galaxy0">
<description>absrel</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_file' absrel_input.fa &&
ln -s '$input_nhx' absrel_input.nhx &&
@HYPHY_INVOCATION@ absrel
--alignment `pwd`/absrel_input.fa
--tree `pwd`/absrel_input.nhx
--code '$gencodeid'
--branches '$branches'
> '$absrel_log'
]]></command>
<inputs>
<expand macro="inputs"/>
<param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
<expand macro="gencode"/>
<expand macro="branches"/>
</inputs>
<outputs>
<data name="absrel_log" format="txt">
<filter>log</filter>
</data>
<data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/>
</outputs>
<tests>
<test>
<param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
<param name="log" value="false"/>
<output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
<description>absrel</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_file' absrel_input.fa &&
ln -s '$input_nhx' absrel_input.nhx &&
@HYPHY_INVOCATION@ absrel
--alignment `pwd`/absrel_input.fa
--tree `pwd`/absrel_input.nhx
--code '$gencodeid'
--branches '$branches'
> '$absrel_log'
]]></command>
<inputs>
<expand macro="inputs"/>
<param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
<expand macro="gencode"/>
<expand macro="branches"/>
</inputs>
<outputs>
<data name="absrel_log" format="txt">
<filter>log</filter>
</data>
<data name="absrel_output" format="hyphy_results.json" from_work_dir="absrel_input.fa.ABSREL.json"/>
</outputs>
<tests>
<test>
<param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
<param name="log" value="false"/>
<output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive random effects branch-site model framework to test whether each branch has evolved under positive selection, using a procedure which infers an optimal number of rate categories per branch.
]]></help>
<expand macro="citations">
<citation type="doi">10.1093/molbev/msv022</citation>
</expand>
]]></help>
<expand macro="citations">
<citation type="doi">10.1093/molbev/msv022</citation>
</expand>
</tool>
225 changes: 112 additions & 113 deletions tools/hyphy/hyphy_bgm.xml
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@@ -1,118 +1,117 @@
<?xml version="1.0"?>
<tool id="hyphy_bgm" name="HyPhy-BGM" version="2.5.0+galaxy0">
<description>- Detecting coevolving sites via Bayesian graphical
models</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_file' bgm_input.fa &&
ln -s '$input_nhx' bgm_input.nhx &&
@HYPHY_INVOCATION@ bgm
--alignment `pwd`/bgm_input.fa
--tree `pwd`/bgm_input.nhx
--run_type $datatype.value
#if $datatype.value == "codon":
--code '$datatype.gencodeid'
#end if
#if $datatype.value == "protein":
--baseline_model '$datatyupe.model'
#end if
--branches '$branch_subset'
--chain '$chain_length'
--burn_in '$burn_in'
--samples '$samples'
--parents '$parents'
--min_subs '$min_sumbs'
> '$bgm_log'
<description>- Detecting coevolving sites via Bayesian graphical models</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_file' bgm_input.fa &&
ln -s '$input_nhx' bgm_input.nhx &&
@HYPHY_INVOCATION@ bgm
--alignment `pwd`/bgm_input.fa
--tree `pwd`/bgm_input.nhx
--run_type $datatype.value
#if $datatype.value == "codon":
--code '$datatype.gencodeid'
#end if
#if $datatype.value == "protein":
--baseline_model '$datatype.model'
#end if
--branches '$branches'
--chain '$chain_length'
--burn_in '$burn_in'
--samples '$samples'
--parents '$parents'
--min_subs '$min_subs'
> '$bgm_log'
]]></command>
<inputs>
<param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
<param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
<conditional name="datatype">
<param name="value" type="select" label="Type of data">
<option value="nucleotide">Nucleotide</option>
<option value="amino-acid">Amino acid</option>
<option value="codon">Codon</option>
</param>
<when value="nucleotide"/>
<when value="amino-acid">
<param name="model" type="select" label="Substitution model">
<option value="LG">LG - Generalist empirical model from
Le and Gascuel (2008)</option>
<option value="HIVBm">HIVBm - Specialist empirical model
for between-host HIV sequences</option>
<option value="HIVWm">HIVWm - Specialist empirical model
for within-host HIV sequences</option>
<option value="WAG">WAG - Generalist empirical model from
Whelan and Goldman (2001)</option>
<option value="JTT">JTT - Generalist empirical model from
Jones, Taylor, and Thornton (1996)</option>
<option value="JC69">JC69 - Generalist empirical model
from with equal exchangeability rates</option>
<option value="mtMet">mtMet - Specialist empirical model
for metazoan mitochondrial genomes</option>
<option value="mtVer">mtVer - Specialist empirical model
for vertebrate mitochondrial genomes</option>
<option value="mtInv">mtInv - Specialist empirical model
for invertebrate mitochondrial genomes</option>
<option value="gcpREV">gcpREV - Specialist empirical
model for green plant chloroplast genomes</option>
<option value="GTR">GTR - General time reversible
model</option>
</param>
</when>
<when value="codon">
<param name="gencodeid" type="select" label="Genetic code">
<option value="Universal">Universal code</option>
<option value="Vertebrate-mtDNA">Vertebrate mitochondrial
DNA code</option>
<option value="Yeast-mtDNA">Yeast mitochondrial DNA
code</option>
<option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
Coelenterate mt; Mycloplasma/Spiroplasma</option>
<option value="Invertebrate-mtDNA">Invertebrate
mitochondrial DNA code</option>
<option value="Ciliate-Nuclear">Ciliate, Dasycladacean
and Hexamita Nuclear code</option>
<option value="Echinoderm-mtDNA">Echinoderm mitochondrial
DNA code</option>
<option value="Euplotid-Nuclear">Euplotid Nuclear
code</option>
<option value="Alt-Yeast-Nuclear">Alternative Yeast
Nuclear code</option>
<option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
code</option>
<option value="Flatworm-mtDNA,">Flatworm mitochondrial
DNA code</option>
<option value="Blepharisma-Nuclear">Blepharisma Nuclear
code</option>
</param>
</when>
</conditional>
<expand macro="branches"/>
<param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
<param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
<param name="sample" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
<param name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node"/>
<param name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis"/>
</inputs>
<outputs>
<data name="bgm_log" format="txt"/>
<data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.bgm.json"/>
</outputs>
<tests>
<test>
<param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
<output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
<inputs>
<param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
<param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
<conditional name="datatype">
<param name="value" type="select" label="Type of data">
<option value="nucleotide">Nucleotide</option>
<option value="amino-acid">Amino acid</option>
<option value="codon">Codon</option>
</param>
<when value="nucleotide"/>
<when value="amino-acid">
<param name="model" type="select" label="Substitution model">
<option value="LG">LG - Generalist empirical model from
Le and Gascuel (2008)</option>
<option value="HIVBm">HIVBm - Specialist empirical model
for between-host HIV sequences</option>
<option value="HIVWm">HIVWm - Specialist empirical model
for within-host HIV sequences</option>
<option value="WAG">WAG - Generalist empirical model from
Whelan and Goldman (2001)</option>
<option value="JTT">JTT - Generalist empirical model from
Jones, Taylor, and Thornton (1996)</option>
<option value="JC69">JC69 - Generalist empirical model
from with equal exchangeability rates</option>
<option value="mtMet">mtMet - Specialist empirical model
for metazoan mitochondrial genomes</option>
<option value="mtVer">mtVer - Specialist empirical model
for vertebrate mitochondrial genomes</option>
<option value="mtInv">mtInv - Specialist empirical model
for invertebrate mitochondrial genomes</option>
<option value="gcpREV">gcpREV - Specialist empirical
model for green plant chloroplast genomes</option>
<option value="GTR">GTR - General time reversible
model</option>
</param>
</when>
<when value="codon">
<param name="gencodeid" type="select" label="Genetic code">
<option value="Universal">Universal code</option>
<option value="Vertebrate-mtDNA">Vertebrate mitochondrial
DNA code</option>
<option value="Yeast-mtDNA">Yeast mitochondrial DNA
code</option>
<option value="Mold-Protozoan-mtDNA">Mold, Protozoan and
Coelenterate mt; Mycloplasma/Spiroplasma</option>
<option value="Invertebrate-mtDNA">Invertebrate
mitochondrial DNA code</option>
<option value="Ciliate-Nuclear">Ciliate, Dasycladacean
and Hexamita Nuclear code</option>
<option value="Echinoderm-mtDNA">Echinoderm mitochondrial
DNA code</option>
<option value="Euplotid-Nuclear">Euplotid Nuclear
code</option>
<option value="Alt-Yeast-Nuclear">Alternative Yeast
Nuclear code</option>
<option value="Ascidian-mtDNA">Ascidian mitochondrial DNA
code</option>
<option value="Flatworm-mtDNA,">Flatworm mitochondrial
DNA code</option>
<option value="Blepharisma-Nuclear">Blepharisma Nuclear
code</option>
</param>
</when>
</conditional>
<expand macro="branches"/>
<param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/>
<param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/>
<param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/>
<param name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node"/>
<param name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis"/>
</inputs>
<outputs>
<data name="bgm_log" format="txt"/>
<data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
</outputs>
<tests>
<test>
<param name="input_file" ftype="fasta" value="bgm-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="bgm-in1.nhx"/>
<output name="bgm_output" file="bgm-out1.json" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
The Bayesian Graphical Model (BGM) method is a tool for detecting coevolutionary interactions between amino acid positions in a protein.
]]></help>
<expand macro="citations">
<citation type="doi">10.1371/journal.pcbi.0030231</citation>
</expand>
]]></help>
<expand macro="citations">
<citation type="doi">10.1371/journal.pcbi.0030231</citation>
</expand>
</tool>
72 changes: 36 additions & 36 deletions tools/hyphy/hyphy_busted.xml
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Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
<?xml version="1.0"?>
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="2.5.0+galaxy0">
<description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_file' busted_input.fa &&
ln -s '$input_nhx' busted_input.nhx &&
@HYPHY_INVOCATION@ busted
--alignment `pwd`/busted_input.fa
--tree `pwd`/busted_input.nhx
--code $gencodeid
--branches '$branches'
> '$busted_log'
]]></command>
<inputs>
<expand macro="inputs"/>
<expand macro="gencode"/>
<expand macro="branches"/>
</inputs>
<outputs>
<data name="busted_log" format="txt"/>
<data name="busted_output" format="hyphy_results.json" from_work_dir="busted_input.fa.BUSTED.json"/>
</outputs>
<tests>
<test>
<param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
<output name="busted_output" file="busted-out1.json" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
<description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
ln -s '$input_file' busted_input.fa &&
ln -s '$input_nhx' busted_input.nhx &&
@HYPHY_INVOCATION@ busted
--alignment `pwd`/busted_input.fa
--tree `pwd`/busted_input.nhx
--code $gencodeid
--branches '$branches'
> '$busted_log'
]]></command>
<inputs>
<expand macro="inputs"/>
<expand macro="gencode"/>
<expand macro="branches"/>
</inputs>
<outputs>
<data name="busted_log" format="txt"/>
<data name="busted_output" format="hyphy_results.json" from_work_dir="busted_input.fa.BUSTED.json"/>
</outputs>
<tests>
<test>
<param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
<output name="busted_output" file="busted-out1.json" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection.
]]></help>
<expand macro="citations">
<citation type="doi">10.1093/molbev/msv035</citation>
</expand>
]]></help>
<expand macro="citations">
<citation type="doi">10.1093/molbev/msv035</citation>
</expand>
</tool>
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