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author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
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1 <tool id="ARGO_beast_run" name="Run BEAST" version="1.0.0">
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2 <description>Perform a discrete trait ancestral reconstruction analysis using BEAST</description>
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3 <requirements>
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4 <requirement type="package" version="0.1">argo_env</requirement>
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5 </requirements>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <command interpreter="bash">
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10 beast.sh ${config}
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11 </command>
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12 <stdio>
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13 <expand macro="basic_errors"/>
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14 </stdio>
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15 <inputs>
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16
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17
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18 <!-- BASIC DATA SPECIFICATION -->
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19 <!-- ======================== -->
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20 <conditional name="alignment">
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21 <param name="specification" type="select" label="Alignment specification"
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22 help="You can either specify your own alignment data, or use the alignment data in the BEAST config file below.">
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23 <option value="file" selected="true">Alignment file</option>
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24 <option value="in_beastfile">Use alignment in BEAST config file</option>
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25 </param>
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26 <when value="file">
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27 <param name="file" type="data" format="fasta" label="Sequence alignment"
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28 help="This is optional if you want to use the alignment in the BEAST config file."/>
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29 </when>
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30 <when value="in_beastfile"/>
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31 </conditional>
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32
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33 <conditional name="metadata">
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34 <param name="specification" type="select" label="Metadata specification"
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35 help="Argo Navis needs to know how sequences split into demes, and whether there is date information.
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36 In this menu, you can specify whether you want to use a CSV metadata file, or regular expressions for extracting this data from sequence names.">
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37 <option value="file" selected="true">Metadata file</option>
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38 <option value="regex">From sequence names</option>
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39 <option value="in_beastfile">Use mappings in BEAST config file</option>
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40 </param>
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41 <when value="file">
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42 <param name="file" type="data" format="csv" label="Metadata file"
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43 help="CSV file specifying deme and (optionally) date data."/>
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44 <param name="deme_column" type="text" label="Deme column" value="deme"
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45 help="Column in CSV file to treat as the deme specification"/>
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46 <param name="date_column" type="text" label="Date column" value="" optional="true"
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47 help="Column in CSV file to treat as the date data. If left blank, all tips are set to time 0 by BEAST."/>
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48 </when>
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49 <!--XXX - Have to tune these regular expressions-->
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50 <when value="regex">
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51 <param name="deme_regex" type="text" value="^[^\s\|]+\|([^\|\s]+)" label="Deme name regular expression"
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52 help="Defaults to second value in a 2-tuple or triple of '|' separated values.
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53 For help working with regular expressions, see rubular.com.
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54 Use () to capture the part of the match you want to extract as the deme name.">
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55 <sanitizer>
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56 <valid initial="string.printable">
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57 <remove value="&apos;"/>
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58 </valid>
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59 <mapping initial="none">
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60 <add source="&apos;" target="__sq__"/>
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61 </mapping>
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62 </sanitizer>
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63 </param>
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64 <param name="date_regex" type="text" value="^[^\s\|]+\|(?:[^\|\s]+)\|([\d]+\.?[\d]*)"
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65 label="Date regular expression" optional="true"
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66 help="This regular expression should extract an integer value, which can be interpreted as a time value.
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67 Whether it is years, months, days (etc.) is up to you.">
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68 <sanitizer>
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69 <valid initial="string.printable">
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70 <remove value="&apos;"/>
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71 </valid>
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72 <mapping initial="none">
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73 <add source="&apos;" target="__sq__"/>
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74 </mapping>
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75 </sanitizer>
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76 </param>
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77 </when>
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78 <when value="in_beastfile">
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79 <!--Nothing-->
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80 </when>
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81 </conditional>
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82
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83 <param name="samples" type="integer" value="10000" label="Number of samples"
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84 help="Number of samples to take."/>
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85 <!--XXX Will have to check to make sure logging frequency is the same between -resume runs-->
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86 <param name="sampling_interval" type="integer" value="1000" label="Sampling interval"
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87 help="Number of states explored in chain between samples."/>
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88 <param name="random_seed" type="integer" value="" label="Random seed" optional="true"
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89 help="Random seed to be used in BEAST MCMC. Specifying and recording this value can aid in reproducibility."/>
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90
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91
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92 <!-- MANUAL BEASTFILE SPECIFICATION -->
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93 <!-- ============================== -->
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94 <conditional name="beastfile">
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95 <param name="specification" type="select" label="BEAST file specification"
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96 help="If you'd like to run a more custom analysis, you can specify your own BEAST file (see detailed help below).
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97 Additionally, if you are performing a resume run, you will need to specify the BEAST file output by the previous run.">
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98 <option value="default" selected="true">Default</option>
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99 <option value="custom">Custom or resume</option>
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100 </param>
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101 <when value="default"/>
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102 <when value="custom">
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103 <param name="template" type="data" format="beastfile" label="BEAST config file"
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104 help="Note that any alignment or deme/date data specified above will override whatever is present in this file.
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105 However, having this data specified in a custom file means you can forgo the inputs above."/>
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106 </when>
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107 </conditional>
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108
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109
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110 <!-- HERE THERE BE DOWNSAMPLING OPTIONS -->
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111 <!-- ================================== -->
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112 <conditional name="downsampling">
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113 <param name="method" type="select" display="radio" label="Downsampling method"
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114 help="Downsampling sets a maximum number of sequences per deme.
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115 This can help you investigate issues of sampling bias and sampling depth.
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116 Random downsampling is recommended for concerns relating to sampling depth, while K-means is recommended for
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117 addressing sampling bias.
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118 Please see the help below for a more detailed information.">
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119 <option value="none" selected="true">None</option>
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120 <option value="random">Random</option>
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121 <option value="kmeans">K-means</option>
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122 </param>
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123 <when value="none">
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124 <!--Do nothing-->
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125 </when>
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126 <when value="random">
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127 <param name="k" type="integer" value="" label="N sequences"
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128 help="Number of sequences to be taken per deme."/>
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129 <param name="random_seed" type="integer" value="" label="Random seed" optional="true"
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130 help="Random seed to be used for sequence selections."/>
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131 </when>
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132 <when value="kmeans">
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133 <param name="k" type="integer" value="" label="N sequences"
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134 help="Number of sequences to be taken per deme."/>
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135 <param name="random_seed" type="integer" value="" label="Random seed" optional="true"
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136 help="Random seed to be used for sequence selections."/>
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137 </when>
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138 </conditional>
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139
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140
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141 <!-- RESUME RUN OPTIONS -->
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142 <!-- ================== -->
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143 <conditional name="resume">
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144 <param name="selector" type="select" label="Resume from a previous run?"
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145 help="If you ran BEAST but found it didn't run long enough, you can resume your run from where you left off.
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146 Note you will need to specify some of the previous run's outputs here and in the 'BEAST file specification' above,
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147 and the only other parameters that will have any effect on the run will be the number of samples.
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148 Note also this probably isn't worth doing if the previous run didn't take very long.">
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149 <option value="false" selected="true">No thanks</option>
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150 <option value="true">Yes please</option>
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151 </param>
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152 <when value="false">
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153 <!--Do nothing-->
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154 </when>
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155 <when value="true">
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156 <param name="logfile" type="data" format="full_logfile" label="Logfile from last run"
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157 help="Cannot be the 'trimmed' output from previous run, but must be the full output."/>
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158 <param name="treefile" type="data" format="full_treefile" label="Treefile from last run"
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159 help="As with the Logfile, cannot be the `trimmed` output."/>
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160 <param name="statefile" type="data" format="statefile" label="State file from previous run."/>
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161 <param name="samples" type="integer" value="10000" label="Number of samples to keep"
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162 help="With resume runs, the log and tree files can grow quite large, bogging down PACT and other analysis tools.
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163 Therefore, after a resume run, 'trimmed' output files are created with this number of samples."/>
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164 </when>
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165 </conditional>
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166
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167 </inputs>
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168
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169 <outputs>
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170 <data name="logfile" format="full_logfile" label="BEAST logfile"/>
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171 <data name="treefile" format="full_treefile" label="BEAST treefile"/>
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172 <data name="statefile" format="statefile" label="BEAST state file"/>
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173 <data name="ess" format="html" label="BEAST effective sample size stats"/>
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174
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175 <data name="formatted_beastfile" format="beastfile" label="BEAST config file">
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176 <filter>resume['selector'] != "true"</filter>
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177 </data>
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178 <data name="downsampled_alignment" format="fasta" label="Downsampled alignment">
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179 <filter>downsampling['method'] != "none"</filter>
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180 </data>
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181 <data name="downsampled_metadata" format="csv" label="Downsampled metadata">
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182 <filter>downsampling['method'] != "none" and metadata['specification'] == "file"</filter>
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183 </data>
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184 <data name="trimmed_logfile" format="trimmed_logfile" label="Trimmed BEAST logfile">
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185 <filter>resume['selector'] == "true"</filter>
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186 </data>
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187 <data name="trimmed_treefile" format="trimmed_treefile" label="Trimmed BEAST treefile">
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188 <filter>resume['selector'] == "true"</filter>
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189 </data>
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190 </outputs>
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191
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192 <configfiles>
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193 <!-- XXX Not sure if these deme specifications will actually work or not ??? -->
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194 <configfile name="config">
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195
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196 ## Specification of alignment
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197 #if $alignment.specification == "file"
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198 ALIGNMENT="${alignment.file}"
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199 #else
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200 ALIGNMENT=""
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201 #end if
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202
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203
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204 METADATA_SPECIFICATION="${metadata.specification}"
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205 #if $metadata.specification == "file"
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206 METADATA_FILE="${metadata.file}"
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207 DEME_COLUMN="${metadata.deme_column}"
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208 #if str($metadata.date_column) not in ["None", ""]
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209 DATE_COLUMN="${metadata.date_column}"
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210 #else
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211 DATE_COLUMN=""
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212 #end if
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213 #elif $metadata.specification == "regex"
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214 DEME_REGEX='${metadata.deme_regex}'
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215 #if str($metadata.date_regex) != 'None'
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216 DATE_REGEX='${metadata.date_regex}'
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217 #else
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218 DATE_REGEX=''
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219 #end if
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220 #else
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221 METADATA_FILE=""
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222 DEME_REGEX=""
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223 DEME_COLUMN=""
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224 DATE_COLUMN=""
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225 DATE_REGEX=""
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226 #end if
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227
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228 SAMPLES_FLAG="-s ${samples}"
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229 SAMPLING_INTERVAL_FLAG="-i ${sampling_interval}"
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230 #if str($random_seed) not in ["None", ""]
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231 RANDOM_SEED_FLAG="-seed ${random_seed}"
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232 #else
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233 RANDOM_SEED_FLAG=""
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234 #end if
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235
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236 BEASTFILE_SPECIFICATION="${beastfile.specification}"
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237 #if $beastfile.specification == "custom"
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238 BEASTFILE_TEMPLATE="${beastfile.template}"
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239 #end if
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240
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241 RESUME_SELECTOR="${resume.selector}"
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242 #if $resume.selector == "true"
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243 RESUME_LOGFILE="${resume.logfile}"
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244 RESUME_TREEFILE="${resume.treefile}"
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245 RESUME_STATEFILE="${resume.statefile}"
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246 RESUME_SAMPLES="${resume.samples}"
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247 #end if
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248
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249 DOWNSAMPLING_METHOD="${downsampling.method}"
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250 #if $downsampling.method != "none"
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251 DOWNSAMPLING_K="${downsampling.k}"
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252 #if str($downsampling.random_seed) != "None"
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253 DOWNSAMPLING_RANDOM_SEED="${downsampling.random_seed}"
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254 #end if
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255 #end if
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256
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257
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258
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259 LOGFILE="${logfile}"
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260 TREEFILE="${treefile}"
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261 ESS="${ess}"
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262
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263 #if $resume.selector != "true"
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264 FORMATTED_BEASTFILE="${formatted_beastfile}"
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265 #else
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266 FORMATTED_BEASTFILE="formatted_beastfile.xml"
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267 #end if
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268 STATEFILE="${statefile}"
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269
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270 #if $downsampling.method != "none"
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271 DOWNSAMPLED_ALIGNMENT="${downsampled_alignment}"
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272 #if $metadata.specification == "file"
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273 DOWNSAMPLED_METADATA="${downsampled_metadata}"
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274 #end if
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275 #end if
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276
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277 #if $resume.selector == "true"
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278 TRIMMED_LOGFILE="${trimmed_logfile}"
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279 TRIMMED_TREEFILE="${trimmed_treefile}"
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280 #end if
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281
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282 </configfile>
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283 </configfiles>
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284
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285 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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286 help-template.rst for examples of commonly-used sections in other Galaxy
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287 tools. -->
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288 <help>
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289
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290 .. class:: infomark
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291
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292
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293 About this tool
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294 ---------------
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295
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296 This tool is your starting point for running an Argo Navis analysis.
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297 It runs BEAST for you, and produces a treefile suitable for running through the Argo Navis PACT tool, which facilitates
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298 visualization and analyses of your data.
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299
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300
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301 Input files
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302 -----------
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303
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304 To run this tool, you'll need some sequence data, and a way to specify which sequences belong to which demes.
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305 The recommended way of doing this is to specify a FASTA file of aligned sequences, and a separate metadata CSV file with
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306 deme specifications.
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307 This metadata file may also be used to specify temporal information for your sequences.
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308 While the column names pointing to the deme and date information are configurable, there must be a "sequence" column
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309 corresponding to the names of the sequences in the FASTA file.
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310 Additionally, there must be no sequences represented in one file not represented in the other.
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311
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312 It is also possible to specify deme and date information directly in the FASTA file sequence names using regular expressions.
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313 To do this, select "From sequence names" from the "Metadata specification" dropdown.
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314 This will open up options for deme and date regular expressions which will be used to extract the information from
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315 the sequence names.
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316 The default behaviour is to parse the sequence names as "|" separated values like this: "name|deme|date".
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317 If you'd like help customizing these regular expressions, please see the `regex tutorial`_ and `rubular`_.
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318
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319 For more custom analyses, you can also specify your own BEAST config file.
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320 This lets you customize model details, priors, and parameters.
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321 If you wish to do this, take a look at the **Customizing your BEAST config file** section below.
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322
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323
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324 Output files
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325 ------------
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326
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327 The following files are created as the result of an Argo Navis BEAST run:
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328
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329 **BEAST logfile**: A standard BEAST logfile of sampled parameters, suitable for analysis with Tracer.
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330
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331 **BEAST treefile**: A nexus file of trees from the posterior, with ancestral states labeled, suitable for
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332 analysis with PACT.
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333
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334 **BEAST effective sample size stats**: Statistics about whether BEAST has run long enough.
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335 You can click on the eye icon next to this file to see this data in-browser.
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336
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337 Once you've carried out a run, you should always check the ESS statistics before doing anything else.
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338 This file will contain a "Recommendation", indicating whether the data is ready to use, or whether you
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339 should run BEAST longer, and if so, how much longer.
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340
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341 While the ESS statistic is an easy way to get a sense for whether your should run BEAST more or not, it's also
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342 a good idea to manually review the logfile using `Tracer`_, before accepting the results as final and
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343 passing them along through the rest of the analysis.
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344 Please see the tutorial in the Introduction for a description of how to do this.
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345
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346
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347 Resume runs
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348 -----------
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349
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350 If you run BEAST and realize it needs to run longer, you can save time by doing a "Resume" run.
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351 This let's you pick up from where you left off, keeping you from having to start over.
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352
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353 Note that in addition to the output files listed above, an initial run of BEAST will also produce the following:
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354
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355 **BEAST config file**: A copy of the BEAST file created for the run.
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356 This has been modified to include sequence, deme, and date information, as well as various other run settings.
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357
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358 **BEAST state file**: This is a file that BEAST maintains as it runs so Resume runs can pick up where they left off.
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359
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360 In order to start a Resume run, start by entering the number of new samples you'd like to add to the data you've already collected.
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361 Next, in the "BEAST file specification" input, select "Custom or Resume".
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362 This will open up a file input from which you can select the BEAST config file from the previous run.
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363 Next, select "Yes" in the "Resume from a previous run?" form input.
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364 This will open up several new input fields where you can specify the logfile, treefile and statefile from your previous run.
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365
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366 You can also specify a total number of samples you want to keep.
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367 When running a Resume run, your log and tree files can grow large enough to bog down analysis tools.
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368 This problem is dealt with by evenly trimming these files to the specified number of samples during Resume runs.
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369 It's important to note, however, that if you do further Resume runs, you must make sure to specify the **untrimmed** log and
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370 tree files for the following runs.
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371 If you don't, bad things will happen (someone will kill a puppy; seriously).
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372
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373 It's also important to note that Resume runs ignore all inputs not explicitly mentioned above.
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374 In particular, you can't change the sequences, the date information, deme specifications or sampling interval for a Resume run.
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375 If you *do* want to change any of this, you must start a new run.
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376
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377
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378 Random seeds
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379 ------------
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380
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381 Both the actual BEAST run and the downsampling methods support specification of random seeds.
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382 Taking advantage of this aids in reproducibility of your analyses, as someone else running with the same data, settings and
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383 random seeds should be able to reproduce the results exactly.
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384 If you choose not to specify your own random seeds, random seeds will be chosen for you and printed out in the logs, so
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385 if you wish to go back and find these values, you can.
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386
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387
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388 Downsampling
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389 ------------
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390
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391 Differences in sampling between demes you study can be a challenge when doing these analyses.
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392 How do you know that one deme having been sampled more deeply isn't artificially biasing the results towards increased
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393 diversity for that deme?
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394 It's also frequently the case that researchers studying viruses don't submit every viral sequence they obtain, but decide
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395 which look "different enough" from the others (and from those already observed) to submit to online repositories.
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396 And typically, the strategy used for deciding which sequences to submit and which not to is not made clear in publications.
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397 As such, treating sequences found in these repositories as an unbiased sample is problematic, and has even greater
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398 potential for introducing diversity bias into your results.
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399
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400 Issues such as these frequently come up in reviewer critiques.
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401 One way to deal with this is to show evidence that the sampling issues aren't significantly affecting the results,
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402 or at the very least, to explore the effects of different sampling strategies on the results.
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403 Argo Navis provides downsampling tools which help you towards this end.
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404
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405 There are two downsampling methods you can use: Random and K-means.
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406 Random downsampling is meant to deal with issues of only sampling depth, while K-means downsampling is meant to
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407 address issues of sampling bias.
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408 While Random downsampling is likely fairly straight-forward, K-means downsampling may not be.
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409
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410 K-means downsampling starts by clustering sequences together into K clusters.
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411 From each of these clusters a single sequence is chosen to represent the entire cluster.
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412 This is done for each deme.
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413 This method introduces intentional, but controlled sampling bias, as for any given number of K samples per
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414 deme, the sequences chosen are going to reflect the *most* diversity possible among those sequences.
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415 While this doesn't *solve* the problem of sampling bias, it does attempt to put all demes on equal footing, by
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416 introducing similar diversity bias in all sequences.
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417
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418 A decent strategy for protecting yourself from reviewers is to use *both* of these methods at various K values,
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419 and compare the results.
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420 Assuming the results look similar in all cases, then great!
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421 It would appear you have a very robust set of conclusions.
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422 If there are differences, there will be a bit more work involved in explaining them, but at least you'll be able to say
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423 you've thoroughly explored the issue.
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424
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425 On a final note, if you *do* decide to use BEAST's downsampling functionality, you will obtain a couple of additional
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426 outputs:
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427
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428 **Downsampled alignment**: The sequences kept in the downsampling process, in FASTA format.
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429
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430 **Downsampled metadata**: If you supplied metadata for the analysis, you will also get a copy of that file containing
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431 metadata for only the sequences kept in the downsampling procedure.
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432
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433 These are not required for any other part of Argo Navis, but are offered for your convenience so you can see which
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434 sequences were chosen and use the same data subsets in other analyses you might perform outside of Argo Navis.
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435
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436
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437 Customizing your BEAST config file
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438 ----------------------------------
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439
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440 Customizing your BEAST config file opens up the full power of BEAST, letting you specify model details, priors, and
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441 other parameters.
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442 If you wish to do this, it's recommended you start by working from this tool's `default BEAST config file`_.
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443 From there, you can specify customizations using the BEAUti program, which is installed alongside BEAST2 (see the
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444 `BEAST2 homepage`_ for downloads).
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445
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446 Before you can load the config file, you'll have to install the BEAST Classic module from within BEAUti.
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447 Simply go to File > Manage Packages, click on "BEAST_CLASSIC", then click "Install".
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448 You can now go to File > Load to select the default BEAST config file.
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449 Once you've made your edits, save your new config file by going to File > Save As.
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450 You can then upload the file into Galaxy by going to Get Data > Upload File within the Galaxy Tool menu, making sure to
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451 specify "beastfile" as the file type.
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452
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453 Once you have your file loaded, select "Custom or resume" from "BEAST file specification", and point the file selector that pops
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454 up to the new config file you just uploaded.
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455 If you wish, you can also tell Argo Navis to use the alignment and deme data in the BEAST config file by selecting the
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456 appropriate options in the "Alignment specification" and "Metadata specification" dropdowns.
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457 If you don't do this, whatever files/options are specified for Sequence alignment and Metadata specification will replace the
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458 data specified in your BEAST config file.
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459
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460 Some notes to keep in mind if you specify your own BEAST config:
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461
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462 1. If you choose to specify the deme/community information directly in the your BEAST file and not apply the CSV or regular
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463 expression data to set this, you must name your discrete trait "deme", even if it refers to something else, like
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464 species name or tissue type.
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465 2. Note that the chain length and sampling interval settings in your BEAST config file will get overridden by whatever is
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466 specified here in this tool, and can not be assumed to remain as specified in your BEAST config file.
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467 3. If you don't have tip dates, you can speed up your run by specifying a custom beast file where your fixed clock's rate isn't
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468 estimated but left constant. If you don't have any temporal data, these estimates won't mean anything anyway.
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469
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470 Note that the default template closely follows the setup in the `Ancestral State Reconstruction tutorial`_ by Remco Bouckaert,
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471 which you can use as a guide for setting up your own custom BEAST analysis.
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472 The `BEAST homepage`_ is also a useful resource if you're looking for help settings things up.
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473
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474
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475
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476 .. _BEAST2 homepage: http://www.beast2.org/
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477 .. _default BEAST config file: http://xxx.doesntexist.yet
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478 .. _regex tutorial: http://regexone.com/lesson/0
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479 .. _rubular: http:rubular.com
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480 .. _Tracer: http://tree.bio.ed.ac.uk/software/tracer/
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481 .. _Ancestral State Reconstruction tutorial: http://beast-classic.googlecode.com/files/ARv2.0.1.pdf
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482 .. _BEAST homepage: http://beast.bio.ed.ac.uk/
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483
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484
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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485 </help>
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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486 </tool>