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hyphy absrel: remove unused log param #4246

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Nov 27, 2021
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hyphy absrel: remove unused log param #4246

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3c8f524
hyphy absrel: remove unused log param
bernt-matthias Nov 26, 2021
f593a50
hyphy fix paramaters in tests that are not in inputs
bernt-matthias Nov 26, 2021
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3 changes: 1 addition & 2 deletions tools/hyphy/hyphy_absrel.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
<description>adaptive Branch Site Random Effects Likelihood</description>
<expand macro="bio_tools"/>
<macros>
Expand All @@ -20,7 +20,6 @@
]]></command>
<inputs>
<expand macro="inputs"/>
<param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
<expand macro="gencode"/>
<param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
<option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
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3 changes: 1 addition & 2 deletions tools/hyphy/hyphy_annotate.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="hyphy_annotate" name="Annotate" version="@VERSION@+galaxy0">
<tool id="hyphy_annotate" name="Annotate" version="@TOOL_VERSION@+galaxy0">
<description>a newick tree with HyPhy</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -29,7 +29,6 @@
<test>
<param name="compressed_msa" ftype="fasta.gz" value="annotate-in1.fa.gz"/>
<param name="input_tree" ftype="nhx" value="annotate-in1.nhx"/>
<param name="multiple_hits" value="None" />
<param name="root" value="REFERENCE" />
<param name="label" value="Annotated" />
<output name="labeled_tree_int" file="annotate-out1-int.nhx" />
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_bgm.xml
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<?xml version="1.0"?>
<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy2" profile="19.09">
<tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy2" profile="19.09">
<description>- Detecting coevolving sites via Bayesian graphical models</description>
<expand macro="bio_tools"/>
<macros>
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8 changes: 5 additions & 3 deletions tools/hyphy/hyphy_busted.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@TOOL_VERSION@+galaxy2" profile="19.09">
<description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
<expand macro="bio_tools"/>
<macros>
Expand Down Expand Up @@ -35,8 +35,10 @@
</test>
<test>
<param name="input_file" ftype="nex" value="busted-in2.nex"/>
<param name="branches" value="specify" />
<param name="branch_label" value="B_US_90_WEAU160" />
<conditional name="branch_cond">
<param name="branch_sel" value="specify"/>
<param name="branch_label" value="B_US_90_WEAU160_BRANCH" />
</conditional>
<param name="srv_options" value="specify" />
<param name="save_alternative_model" value="true" />
<output name="busted_output" file="busted-out2-1.json" compare="sim_size"/>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_cfel.xml
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<?xml version="1.0"?>
<tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_cfel" name="HyPhy-CFEL" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_conv.xml
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<?xml version="1.0"?>
<tool id="hyphy_conv" name="HyPhy-Conv" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_conv" name="HyPhy-Conv" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>translate an in-frame codon alignment to proteins</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_fade.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_fade" name="HyPhy-FADE" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>: FUBAR* Approach to Directional Evolution (*Fast
Unconstrained Bayesian Approximation)</description>
<expand macro="bio_tools"/>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_fel.xml
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<?xml version="1.0"?>
<tool id="hyphy_fel" name="HyPhy-FEL" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Fixed Effects Likelihood</description>
<expand macro="bio_tools"/>
<macros>
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6 changes: 4 additions & 2 deletions tools/hyphy/hyphy_fubar.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Fast Unconstrained Bayesian AppRoximation</description>
<expand macro="bio_tools"/>
<macros>
Expand Down Expand Up @@ -34,7 +34,9 @@
<test>
<param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/>
<param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/>
<param name="posterior" value="Variational-Bayes"/>
<conditional name="posteriorEstimationMethod">
<param name="method" value="Variational-Bayes"/>
</conditional>
<output name="fubar_output" file="fubar-out1.json" compare="sim_size"/>
</test>
</tests>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_gard.xml
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<?xml version="1.0"?>
<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_gard" name="HyPhy-GARD" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Genetic Algorithm for Recombination Detection</description>
<expand macro="bio_tools"/>
<macros>
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6 changes: 4 additions & 2 deletions tools/hyphy/hyphy_meme.xml
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<?xml version="1.0"?>
<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy2" profile="19.09">
<tool id="hyphy_meme" name="HyPhy-MEME" version="@TOOL_VERSION@+galaxy2" profile="19.09">
<description>Mixed Effects Model of Evolution</description>
<expand macro="bio_tools"/>
<macros>
Expand Down Expand Up @@ -32,7 +32,9 @@
<test>
<param name="input_file" ftype="fasta" value="meme-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
<param name="branches" value="All"/>
<conditional name="branch_cond">
<param name="branch_sel" value="All"/>
</conditional>
<param name="p_value" value="0.1"/>
<output name="meme_output" file="meme-out1.json" compare="sim_size" delta="25000"/>
</test>
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6 changes: 4 additions & 2 deletions tools/hyphy/hyphy_prime.xml
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<?xml version="1.0"?>
<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_prime" name="HyPhy-PRIME" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Property Informed Models of Evolution</description>
<expand macro="bio_tools"/>
<macros>
Expand Down Expand Up @@ -37,7 +37,9 @@
<test>
<param name="input_file" ftype="fasta" value="prime-in1.fa"/>
<param name="input_nhx" ftype="nhx" value="prime-in1.nhx"/>
<param name="branches" value="All"/>
<conditional name="branch_cond">
<param name="branch_sel" value="All"/>
</conditional>
<param name="p_value" value="0.1"/>
<param name="prop_set" value="Atchley"/>
<output name="prime_output" file="prime-out1.json" compare="sim_size"/>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_relax.xml
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<?xml version="1.0"?>
<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_relax" name="HyPhy-RELAX" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Detect relaxed selection in a codon-based
phylogenetic framework</description>
<expand macro="bio_tools"/>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_slac.xml
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<?xml version="1.0"?>
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_slac" name="HyPhy-SLAC" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Single Likelihood Ancestor Counting</description>
<expand macro="bio_tools"/>
<macros>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_sm19.xml
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<?xml version="1.0"?>
<tool id="hyphy_sm19" name="HyPhy-SM2019" version="@VERSION@+galaxy1" profile="19.09">
<tool id="hyphy_sm19" name="HyPhy-SM2019" version="@TOOL_VERSION@+galaxy1" profile="19.09">
<description>Partition Tree using Modified Slatkin-Maddison Test</description>
<expand macro="bio_tools"/>
<macros>
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2 changes: 1 addition & 1 deletion tools/hyphy/hyphy_strike_ambigs.xml
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<?xml version="1.0"?>
<tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@VERSION@">
<tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@TOOL_VERSION@">
<description>in a multiple alignment using HyPhy</description>
<macros>
<import>macros.xml</import>
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4 changes: 2 additions & 2 deletions tools/hyphy/macros.xml
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Expand Up @@ -144,10 +144,10 @@
<yield/>
</citations>
</xml>
<token name="@VERSION@">2.5.31</token>
<token name="@TOOL_VERSION@">2.5.31</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@VERSION@">hyphy</requirement>
<requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
<yield/>
</requirements>
</xml>
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2 changes: 1 addition & 1 deletion tools/hyphy/test-data/busted-in2.nex
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Expand Up @@ -26,5 +26,5 @@ MATRIX
END;

BEGIN TREES;
TREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160));
TREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160{B_US_90_WEAU160_BRANCH}));
END;
199 changes: 115 additions & 84 deletions tools/hyphy/test-data/busted-out2-1.json
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