Mercurial > repos > iuc > hyphy_absrel

annotate hyphy_absrel.xml @ 35:aa96474b3a87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 14:59:00 +0000
parents 68916eb8887f
children 16093bcfe525
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>adaptive Branch Site Random Effects Likelihood</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 ln -s '$absrel_output' ${input_file}.aBSREL.json &&
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11 @HYPHYMPI@ absrel
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12 --alignment ./$input_file
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13 @INPUT_TREE@
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14 --code '$gencodeid'
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15 @branch_options@
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16 --output '$absrel_output'
16
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17 --multiple-hits $multiple_hits
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18 $srv
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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 <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions">
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25 <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
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26 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
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27 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
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28 </param>
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29 <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />
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30 <expand macro="branches"/>
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31 </inputs>
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32 <outputs>
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33 <data name="absrel_output" format="hyphy_results.json" />
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34 </outputs>
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35 <tests>
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36 <test>
1
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37 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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38 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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39 <param name="multiple_hits" value="None" />
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40 <output name="absrel_output">
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41 <assert_contents>
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42 <has_size value="10512" delta="100"/>
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43 <has_text text="fits"/>
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44 <has_text text="branch attributes"/>
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45 <has_text text="Full adaptive model"/>
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46 </assert_contents>
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47 </output>
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48 <assert_stdout>
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49 <has_text text="found **2** branches under selection among **5** tested"/>
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50 </assert_stdout>
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51 </test>
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52 <test>
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53 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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54 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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55 <param name="multiple_hits" value="Double" />
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56 <output name="absrel_output">
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57 <assert_contents>
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58 <has_size value="11117" delta="100"/>
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59 <has_text text="fits"/>
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60 <has_text text="branch attributes"/>
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61 <has_text text="Full adaptive model"/>
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62 </assert_contents>
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63 </output>
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64 <assert_stdout>
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65 <has_text text="found **0** branches under selection among **5** tested"/>
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66 </assert_stdout>
0
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67 </test>
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68 <test>
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69 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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70 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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71 <param name="multiple_hits" value="Double" />
35
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72 <param name="srv" value="true" />
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73 <output name="absrel_output">
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74 <assert_contents>
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75 <has_size value="23396" delta="100"/>
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76 <has_text text="fits"/>
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77 <has_text text="branch attributes"/>
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78 <has_text text="Full adaptive model"/>
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79 </assert_contents>
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80 </output>
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81 <assert_stdout>
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82 <has_text text="found **0** branches under selection among **5** tested"/>
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83 </assert_stdout>
33
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84 </test>
0
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85 </tests>
1
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86 <help><![CDATA[
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87
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88 aBSREL : Adaptive Branch-Site Random Effects Likelihood
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89 =======================================================
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90
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91 What question does this method answer?
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92 --------------------------------------
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93
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94 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?
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95
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96 Recommended Applications
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97 ------------------------
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98
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99 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
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100 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences)
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101
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102 Brief description
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103 -----------------
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104
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105 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
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106 random effects branch-site model framework to test whether each branch
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107 has evolved under positive selection, using a procedure which infers an
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108 optimal number of rate categories per branch.
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109
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110
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111 Input
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112 -----
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113
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114 1. A *FASTA* sequence alignment.
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115 2. A phylogenetic tree in the *Newick* format
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116
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117 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
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118
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119
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120 Output
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121 ------
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122
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123 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
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124
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125 For each tested branch the analysis will infer the appropriate number of selective regimes,
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126 and whether or not there is statistical evidence of positive selection on that branch.
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127
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128 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)
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129
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130 Further reading
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131 ---------------
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132
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133 http://hyphy.org/methods/selection-methods/#absrel
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134
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135
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136 Tool options
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137 ------------
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138 ::
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139
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140
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141 --code Which genetic code to use
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142
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143 --branches Which branches should be tested for selection?
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144 All [default] : test all branches
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145
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146 Internal : test only internal branches (suitable for
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147 intra-host pathogen evolution for example, where terminal branches
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148 may contain polymorphism data)
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149
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150 Leaves: test only terminal (leaf) branches
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151
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152 Unlabeled: if the Newick string is labeled using the {} notation,
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153 test only branches without explicit labels
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154 (see http://hyphy.org/tutorials/phylotree/)
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155
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156
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157
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158 ]]></help>
0
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159 <expand macro="citations">
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160 <citation type="doi">10.1093/molbev/msv022</citation>
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161 </expand>
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162 </tool>