Mercurial > repos > iuc > breseq

annotate breseq.xml @ 2:82fb5e3bb93e draft

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"planemo upload commit 9f3f6fbbe2653d4c42818a89d6897ddaef6706b1"
author iuc
date Wed, 07 Apr 2021 12:17:45 +0000
parents 85c57cc9b558
children 0d18a3ba2d1c
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1 <tool id="breseq" name="breseq" version="@PACKAGE_VERSION@+@GALAXY_VERSION@">
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2
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3 <description>find mutations in haploid microbial genomes</description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="0.35.5">breseq</requirement>
1
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11 <requirement type="package" version="1.32">tar</requirement>
0
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12 </requirements>
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13
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14 <version_command>breseq --version</version_command>
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15
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16 <command detect_errors="aggressive">
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17 <![CDATA[
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18 #set $ref_opts = ""
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19 #for $i, $r in enumerate( $references ):
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20 #if str($references[$i].reference.source) == "history":
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21 #for $ref in $references[$i].reference.own_genome:
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22 #if $ref
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23 #set $ref_opts = $ref_opts + " --reference '" + str($ref) + "'"
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24 #end if
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25 #end for
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26 #else:
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27 #set $ref_opts = $ref_opts + " --reference '" + $references[$i].reference.fixed_genome.fields.path + "'"
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28 #end if
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29 #end for
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30
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31 #if str($run.mode) == 'detect'
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32 breseq
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33
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34 --num-processors \${GALAXY_SLOTS:-4}
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35
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36 -o results
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37
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38 $ref_opts
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39
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40 #for $s in $run.fastqs:
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41 ${s}
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42 #end for
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43
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44 #if $run.name
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45 --name '$run.name'
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46 #end if
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47
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48 $run.polymorphism_prediction
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49 $run.predict_junctions
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50
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51 #if 'gd' in str($run.output_options.formats).split(','):
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52 && cp results/output/output.gd '$output'
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53 #end if
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54
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55 #if 'html' in str($run.output_options.formats).split(','):
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56 && cp results/output/index.html '$report'
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57 && mkdir $report.extra_files_path
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58 && cp -R results/output/* $report.extra_files_path
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59 #end if
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60
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61 #if 'zip' in str($run.output_options.formats).split(','):
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62 && tar -zcf '$zip_output' results
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63 #end if
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64
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65 #if 'log' in str($run.output_options.formats).split(','):
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66 && cp results/output/log.txt '$log'
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67 #end if
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68 #else
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69 #set $first = 1
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70 #for $o in str($run.output_options.formats).split(','):
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71
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72 #if $first == 0
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73 &&
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74 #end if
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75 #set $first = 0
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76
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77 gdtools ANNOTATE
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78
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79 --format '$o'
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80
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81 -o
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82 #if $o == 'html':
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83 '$annreport'
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84 #else if $o == 'gd':
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85 '$genomediff'
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86 #else if $o == 'tsv':
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87 '$tabdelim'
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88 #else if $o == 'phylip':
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89 '$phylipout'
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90 #else if $o == 'json':
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91 '$jsonout'
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92 #end if
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93
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94 $ref_opts
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95
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96 #for $s in $run.gds:
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97 ${s}
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98 #end for
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99 #end for
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100 #end if
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101 ]]>
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102 </command>
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103
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104 <inputs>
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105 <repeat name="references" title="Reference Genome" min="1">
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106 <conditional name="reference">
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107 <param name="source" type="select" label="Reference source" >
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108 <option value="builtin">built-in</option>
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109 <option value="history" selected="true">history</option>
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110 </param>
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111 <when value="builtin">
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112 <param name="fixed_genome" argument="--reference" type="select" optional="false" label="Galaxy Built-in Reference(s)">
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113 <options from_data_table="genbank_files">
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114 <filter type="sort_by" column="3"/>
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115 <validator type="no_options" message="No built-in genbank records have been configured"/>
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116 </options>
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117 </param>
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118 </when>
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119 <when value="history">
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120 <param name="own_genome" argument="--reference" type="data" format="fasta,genbank" multiple="true" optional="false" label="Fasta or Genbank Reference(s)" />
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121 </when>
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122 </conditional>
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123 </repeat>
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124
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125 <conditional name="run">
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126 <param name="mode" type="select" label="Run Mode" help="Detect, annotate, or compare variants.">
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127 <option value="detect" selected="true">Detect</option>
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128 <option value="annotate">Annotate</option>
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129 <option value="compare">Compare</option>
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130 </param>
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131 <when value="detect">
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132
2
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133 <param name="fastqs" type="data" format="fastq,fastq.gz" multiple="true" label="Fastq Read Files" />
0
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134
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135 <param argument="--polymorphism-prediction" name="polymorphism_prediction" type="select" label="Detection Mode" help="**Polymorphism mode**: Detect variants with frequencies between 0% and 100% if a mixture model is well-supported by the read alignment evidence. Use to analyze a mixed population of genomes evolved from a common ancestor. **Consensus mode**: Detect variants present in 100% of the sample. Use when re-sequencing a clonal haploid genome. This mode is the default.">
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136 <option value="" selected="true">Consensus</option>
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137 <option value="--polymorphism-prediction">Polymorphism</option>
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138 </param>
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139
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140 <param name="name" argument="--name" type="text" value="" label="Analysis Name" help="Human-readable name of the analysis run for output (DEFAULT=none)." />
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141
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142 <param name="predict_junctions" type="boolean" truevalue="" falsevalue="--no-junction-prediction" checked="true" label="Predict Junctions" help="Predict new sequence junctions (default). --no-junction-prediction is supplied if 'No' is selected. Otherwise, there is no flag." />
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143
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144 <section name="output_options" title="Output Options" expanded="false">
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145 <param name="formats" type="select" multiple="true" optional="false" display="checkboxes" label="Output Formats">
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146 <option value="gd" selected="true">Variants (GenomeDiff)</option>
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147 <option value="html">Variant Report (Webpage)</option>
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148 <option value="zip">All Variant Results (Gzip)</option>
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149 <option value="log">Log (Text)</option>
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150 </param>
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151 </section>
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152
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153 </when>
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154 <when value="annotate">
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155
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156 <param name="gds" type="data" format="tabular" multiple="true" optional="false" label="GenomeDiff (gd) Files" help="Files as produced by breseq" />
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157
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158 <expand macro="annotate_format_opts">
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159 <option value="gd" selected="true">Annotated Variants (GenomeDiff)</option>
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160 </expand>
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161
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162 </when>
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163 <when value="compare">
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164
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165 <param name="gds" type="data" format="tabular" multiple="true" optional="false" label="GenomeDiff (gd) Files" help="Files as produced by breseq" min="2" />
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166
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167 <expand macro="annotate_format_opts">
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168 <option value="phylip" selected="true">Variant Comparison (Phylip)</option>
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169 <option value="gd">Annotated Variants (GenomeDiff)</option>
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170 </expand>
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171
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172 </when>
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173 </conditional>
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174
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175 </inputs>
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176
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177 <outputs>
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178 <data format="html" name="report" label="${tool.name} on ${on_string}: Variants (Webpage)">
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179 <filter>run['mode'] == 'detect' and 'html' in run['output_options']['formats']</filter>
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180 </data>
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181 <data format="html" name="annreport" label="${tool.name} on ${on_string}: Annotated Variants Report (Webpage)">
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182 <filter>run['mode'] != 'detect' and 'html' in run['output_options']['formats']</filter>
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183 </data>
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184
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185 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Variants (GenomeDiff)">
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186 <filter>run['mode'] == 'detect' and 'gd' in run['output_options']['formats']</filter>
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187 </data>
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188 <data format="tabular" name="genomediff" label="${tool.name} on ${on_string}: Annotated Variants (GenomeDiff)">
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189 <filter>run['mode'] != 'detect' and 'gd' in run['output_options']['formats']</filter>
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190 </data>
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191
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192 <data format="zip" name="zip_output" label="${tool.name} on ${on_string}: All Variant Results (Gzip)">
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193 <filter>'zip' in run['output_options']['formats']</filter>
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194 </data>
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195 <data format="txt" name="log" label="${tool.name} on ${on_string}: Breseq Log">
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196 <filter>'log' in run['output_options']['formats']</filter>
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197 </data>
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198 <data format="tabular" name="tabdelim" label="${tool.name} on ${on_string}: Annotated Variants (Tabular)">
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199 <filter>'tsv' in run['output_options']['formats']</filter>
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200 </data>
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201 <data format="phylip" name="phylipout" label="${tool.name} on ${on_string}: Variant Comparison (Phylip)">
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202 <filter>'phylip' in run['output_options']['formats']</filter>
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203 </data>
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204 <data format="txt" name="jsonout" label="${tool.name} on ${on_string}: Annotated Variants (JSON)">
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205 <filter>'json' in run['output_options']['formats']</filter>
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206 </data>
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207 </outputs>
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208
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209 <tests>
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210 <test>
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211 <repeat name="references">
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212 <conditional name="reference">
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213 <param name="source" value="history" />
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214 <param name="own_genome" value="lambda.gbk" />
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215 </conditional>
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216 </repeat>
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217 <conditional name="run">
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218 <param name="mode" value="detect" />
2
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219 <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz" />
0
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220 <param name="polymorphism_prediction" value="" />
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221 <param name="name" value="smallest" />
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222 <param name="predict_junctions" value="" />
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223 <section name="output_options">
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224 <param name="formats" value="html,log,gd,zip" />
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225 </section>
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226 </conditional>
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227
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228 <output name="report" file="report.html" compare="sim_size" delta="100" />
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229 <output name="log" file="log.txt" lines_diff="4">
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230 <assert_contents>
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231 <has_text text="breseq --num-processors" />
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232 </assert_contents>
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233 </output>
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234 <output name="output" file="gdout.txt" lines_diff="8" />
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235 <output name="zip_output">
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236 <assert_contents>
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237 <has_archive_member path="results/output/output.gd" />
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238 </assert_contents>
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239 </output>
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240 </test>
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241 <test>
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242 <repeat name="references">
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243 <conditional name="reference">
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244 <param name="source" value="builtin" />
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245 <param name="fixed_genome" value="lambda1" />
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246 </conditional>
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247 </repeat>
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248 <conditional name="run">
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249 <param name="mode" value="detect" />
2
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250 <param name="fastqs" value="lambda.short_sequence_repeats.fastq.gz" ftype="fastq.gz"/>
0
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251 <param name="polymorphism_prediction" value="" />
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252 <param name="name" value="smallest" />
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253 <param name="predict_junctions" value="" />
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254 <section name="output_options">
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255 <param name="formats" value="gd" />
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256 </section>
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257 </conditional>
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258
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259 <output name="output" file="gdout.txt" lines_diff="8" />
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260 </test>
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261 <test>
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262 <repeat name="references">
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263 <conditional name="reference">
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264 <param name="source" value="history" />
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265 <param name="own_genome" value="lambda.gbk" />
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266 </conditional>
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267 </repeat>
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268 <conditional name="run">
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269 <param name="mode" value="annotate" />
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270 <param name="gds" value="gdout.txt" />
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271 <section name="output_options">
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272 <param name="formats" value="html" />
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273 </section>
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274 </conditional>
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275
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276 <output name="annreport" file="gdtoolsout.html" compare="sim_size" delta="100" />
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277 </test>
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278 </tests>
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279
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280 <help>
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281 <![CDATA[
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282 **Detect Variants**
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283
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284 breseq (pronounced: \\brēz-ˈsēk\\ or breeze-seq) is a computational pipeline for
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285 the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent,
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286 etc.). It uses reference-based alignment approaches to predict mutations in a
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287 sample relative to an already sequenced genome. breseq is intended for microbial
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288 genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from
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289 the reference sequence (<1 mutation per 1000 bp).
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290
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291 breseq's primary advantages over other software programs are that it can:
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292
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293 - Accurately predict new sequence junctions, such as those associated with mobile element insertions.
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294 - Integrate multiple sources of evidence for genetic changes into mutation predictions.
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295 - Produce annotated output describing biologically relevant mutational events.
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296
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297 breseq was initially developed to analyze data from the Lenski long-term
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298 evolution experiment with `E. coli`_. References: barrick2009a_ barrick2009b_.
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299
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300 .. _`E. coli`: http://myxo.css.msu.edu/ecoli/
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301 .. _barrick2009a: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009a
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302 .. _barrick2009b: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009b
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303
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304 However, breseq may be generally useful to researchers who are:
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305
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306 - Tracking mutations over time in microbial evolution experiments.
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307 - Checking strains for unwanted second-site mutations after genetic manipulations.
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308 - Identifying mutations that occur during strain improvement or after long-term culture of engineered strains.
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309 - Discovering what mutations arise in pathogens during infection or cause antibiotic resistance.
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310
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311
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312 *Inputs*
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313
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314 Breseq accepts files in FASTQ format. It does not take pair-end information into
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315 account.
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316
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317 You can either run in clonal (consensus) mode or search for polymorphisms in a
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318 population.
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319
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320 You can also select an external sequence (eg. a transposon) to detect for
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321 insertions or horizontal transfer.
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322
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323
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324 *Outputs*
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325
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326 Breseq outputs a number of files. These are all condensed in a single zipped
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327 file.
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328
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329 It contains output files with the final results, accessible through
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330 ``output/index.html``
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331
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332 It also contains data files with accessory data, including:
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333
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334 - ``data/reference.fasta`` (file with reference genome: can be used in eg. IGV browser)
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335 - ``data/reference.gff`` (file with genomic annotations: can be used in eg. IGV browser)
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336 - ``data/areference.bam`` (file with read alignments: can be used in eg. IGV browser)
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337 - ``data/unmatched.*`` (files with read that failed to align: can be used to build an assembly or to eg. blast against NCBI)
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338
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339
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340 ----
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341
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342 **Annotate Variants**
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343
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344 Annotate a GenomeDiff file (generated by breseq) with information about
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345 mutations (what genes they affect, amino acid substitutions, etc.) If multiple
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346 input files are provided, then also COMPARE the frequencies for identical
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347 mutations across samples.
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348 ]]>
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349 </help>
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350
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351 <citations>
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352 <citation type="doi">10.1007/978-1-4939-0554-6_12</citation>
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353 </citations>
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354
1
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355 </tool>