Mercurial > repos > iuc > hyphy_slac

annotate hyphy_slac.xml @ 36:183cf2baf56e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:40:22 +0000
parents 6130cd31dfb9
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1 <tool id="hyphy_slac" name="HyPhy-SLAC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Single Likelihood Ancestor Counting</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @SYMLINK_FILES@
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10 @HYPHYMP@ slac
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11 --alignment ./$input_file
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12 @INPUT_TREE@
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13 --code '$gencodeid'
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14 @branch_options@
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15 --samples '$number_of_samples'
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16 --pvalue '$p_value'
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17 --output '$slac_output'
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18 --kill-zero-lengths $kill_zero_lengths > slac_stdout.md
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19 @ERRORS@
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20 ]]></command>
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21 <inputs>
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22 <expand macro="inputs"/>
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23 <expand macro="gencode"/>
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24 <expand macro="branches"/>
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25 <param argument="--pvalue" name="p_value" type="float" value=".1" min="0" max="1" label="P-value" />
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26 <param argument="--samples" name="number_of_samples" type="integer" value="0" min="0" max="10000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
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27 <expand macro="kill_zero_lengths_param"/>
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28 </inputs>
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29 <outputs>
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30 <data name="slac_md_report" format="markdown" from_work_dir="slac_stdout.md" label="SLAC Report (Markdown) for ${tool.name} on ${on_string}" />
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31 <data name="slac_output" format="hyphy_results.json" />
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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36 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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37 <param name="number_of_samples" value="100"/>
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38 <output name="slac_output">
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39 <assert_contents>
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40 <has_text text="sample-2.5"/>
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41 <has_text text="sample-97.5"/>
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42 <has_text text="Global MG94xREV"/>
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43 </assert_contents>
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44 </output>
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45 <output name="slac_md_report">
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46 <assert_contents>
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47 <has_text text="Performing joint maximum likelihood ancestral state reconstruction"/>
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48 <has_text text="Selected 5 branches to include in SLAC calculations: `Pig, Cow, Node2, Baboon, Rat`"/>
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49 </assert_contents>
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50 </output>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 SLAC : Single Likelihood Ancestor Counting
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55 ==========================================
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57 What question does this method answer?
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58 --------------------------------------
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59
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60 SLAC (Single Likelihood Ancestor Counting) is designed to identify individual sites within a gene that are subject to pervasive diversifying selection, meaning selection that acts consistently across the entire evolutionary phylogeny. It helps answer: Which specific sites in a gene show evidence of positive selection that has been maintained throughout the evolutionary history of the analyzed sequences?
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62 Recommended Applications
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63 ------------------------
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65 The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
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66 (or balancing selection), including adaptive immune escape by viruses. As such, SLAC is ideally suited to identify sites under positive selection which
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67 represent candidate sites subject to strong selective pressures across the entire phylogeny.
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68 SLAC provides legacy functionality as a counting-based method adapted for phylogenetic applications.
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69 In general, this method will be the least statistically robust (compared to FEL or FUBAR), but it is the most directly interpretable.
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71 Brief description
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72 -----------------
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73
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74 SLAC (Single Likelihood Ancestor Counting) is a counting-based method designed to detect pervasive positive or negative selection at individual sites within a gene. It operates by first inferring ancestral sequences at each node of the provided phylogenetic tree using a maximum likelihood approach. This reconstruction allows for the estimation of synonymous (dS) and non-synonymous (dN) substitution rates at each site across the entire phylogeny. Finally, a binomial test is applied to determine if the observed number of non-synonymous substitutions significantly deviates from the expected number under neutrality (dN = dS). The method aggregates information across all branches of the phylogeny, making it suitable for detecting pervasive diversifying selection (dN > dS) or purifying selection (dN < dS) that acts consistently throughout the evolutionary history of the analyzed sequences. While generally less statistically robust than likelihood-based methods like FEL or FUBAR, SLAC offers direct interpretability of its results.
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76 How it works
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77 ------------
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79 1. Ancestral Sequence Reconstruction: SLAC begins by reconstructing the most likely ancestral sequences at each internal node of the provided phylogenetic tree.
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80 2. Counting Substitutions: Once ancestral sequences are inferred, the method counts the number of synonymous (dS) and non-synonymous (dN) substitutions that have occurred along each branch of the phylogeny.
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81 3. Binomial Test: For each site, SLAC applies a binomial test. The null hypothesis is that non-synonymous and synonymous mutations occur at equal rates (i.e., no selection).
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82 4. Pervasive Selection: By aggregating evidence across all branches of the tree, SLAC identifies sites that have been under consistent selective pressure throughout the evolutionary history of the gene.
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83
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84 Input
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85 -----
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86
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87 1. A coding multiple sequence alignment.
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88 2. A phylogenetic tree in the *Newick* format
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89
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90 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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91
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92
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93 Output
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94 ------
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95
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96 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). This JSON output can be visualized using the HyPhy Vision platform at http://vision.hyphy.org/SLAC/.
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97
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98 Further reading
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99 ---------------
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100
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101 http://hyphy.org/methods/selection-methods/#SLAC
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102
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103
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104 Tool options
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105 ------------
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106 ::
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107
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108 --alignment [required] An in-frame codon alignment in one of the formats supported by HyPhy.
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109 --tree [conditionally required] A phylogenetic tree (optionally annotated with {}).
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110
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111 --code Which genetic code to use (see tool form for available options).
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112
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113 --branches Which branches should be tested for selection?
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114 All [default] : test all branches
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115 Internal : test only internal branches (suitable for intra-host pathogen evolution for example, where terminal branches may contain polymorphism data)
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116 Leaves: test only terminal (leaf) branches
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117 Unlabeled: if the Newick string is labeled using the {} notation, test only branches without explicit labels (see http://hyphy.org/tutorials/phylotree/)
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118 Custom : Enter a branch label.
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119
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120 --pvalue The significance level used to determine significance (default: 0.1, range: 0 to 1).
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121 --samples Draw this many alternative ancestral state reconstructions to evaluate uncertainty (default: 100, range: 0 to 10000).
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122
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123 --kill-zero-lengths Automatically delete internal zero-length branches for computational efficiency.
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124 Yes [default] : Automatically delete internal zero-length branches for computational efficiency (will not affect results otherwise).
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125 Constrain : Keep zero-length branches, but constrain their values to 0.
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126 No : Keep all branches.
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127
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128 ]]>
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129 </help>
0
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130 <expand macro="citations">
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131 <citation type="doi">10.1093/molbev/msi105</citation>
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132 </expand>
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133 </tool>