Mercurial > repos > iuc > breseq

annotate breseq.xml @ 0:f848a7f97332 draft

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"planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
author iuc
date Thu, 31 Oct 2019 19:40:40 -0400
parents
children 85c57cc9b558
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0
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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="0.34.0">breseq</requirement>
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11 </requirements>
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12
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13 <version_command>breseq --version</version_command>
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14
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15 <command detect_errors="aggressive">
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16 <![CDATA[
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17 #set $ref_opts = ""
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18 #for $i, $r in enumerate( $references ):
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19 #if str($references[$i].reference.source) == "history":
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20 #for $ref in $references[$i].reference.own_genome:
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21 #if $ref
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22 #set $ref_opts = $ref_opts + " --reference '" + str($ref) + "'"
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23 #end if
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24 #end for
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25 #else:
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26 #set $ref_opts = $ref_opts + " --reference '" + $references[$i].reference.fixed_genome.fields.path + "'"
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27 #end if
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28 #end for
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29
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30 #if str($run.mode) == 'detect'
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31 breseq
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32
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33 --num-processors \${GALAXY_SLOTS:-4}
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34
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35 -o results
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36
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37 $ref_opts
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38
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39 #for $s in $run.fastqs:
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40 ${s}
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41 #end for
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42
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43 #if $run.name
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44 --name '$run.name'
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45 #end if
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46
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47 $run.polymorphism_prediction
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48 $run.predict_junctions
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49
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50 #if 'gd' in str($run.output_options.formats).split(','):
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51 && cp results/output/output.gd '$output'
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52 #end if
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53
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54 #if 'html' in str($run.output_options.formats).split(','):
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55 && cp results/output/index.html '$report'
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56 && mkdir $report.extra_files_path
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57 && cp -R results/output/* $report.extra_files_path
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58 #end if
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59
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60 #if 'zip' in str($run.output_options.formats).split(','):
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61 && tar -zcf '$zip_output' results
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62 #end if
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63
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64 #if 'log' in str($run.output_options.formats).split(','):
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65 && cp results/output/log.txt '$log'
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66 #end if
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67 #else
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68 #set $first = 1
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69 #for $o in str($run.output_options.formats).split(','):
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70
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71 #if $first == 0
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72 &&
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73 #end if
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74 #set $first = 0
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75
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76 gdtools ANNOTATE
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77
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78 --format '$o'
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79
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80 -o
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81 #if $o == 'html':
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82 '$annreport'
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83 #else if $o == 'gd':
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84 '$genomediff'
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85 #else if $o == 'tsv':
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86 '$tabdelim'
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87 #else if $o == 'phylip':
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88 '$phylipout'
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89 #else if $o == 'json':
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90 '$jsonout'
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91 #end if
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92
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93 $ref_opts
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94
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95 #for $s in $run.gds:
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96 ${s}
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97 #end for
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98 #end for
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99 #end if
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100 ]]>
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101 </command>
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102
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103 <inputs>
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104 <repeat name="references" title="Reference Genome" min="1">
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105 <conditional name="reference">
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106 <param name="source" type="select" label="Reference source" >
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107 <option value="builtin">built-in</option>
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108 <option value="history" selected="true">history</option>
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109 </param>
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110 <when value="builtin">
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111 <param name="fixed_genome" argument="--reference" type="select" optional="false" label="Galaxy Built-in Reference(s)">
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112 <options from_data_table="genbank_files">
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113 <filter type="sort_by" column="3"/>
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114 <validator type="no_options" message="No built-in genbank records have been configured"/>
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115 </options>
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116 </param>
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117 </when>
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118 <when value="history">
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119 <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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120 </when>
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121 </conditional>
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122 </repeat>
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123
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124 <conditional name="run">
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125 <param name="mode" type="select" label="Run Mode" help="Detect, annotate, or compare variants.">
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126 <option value="detect" selected="true">Detect</option>
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127 <option value="annotate">Annotate</option>
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128 <option value="compare">Compare</option>
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129 </param>
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130 <when value="detect">
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131
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132 <param name="fastqs" type="data" format="fastq" multiple="true" label="Fastq Read Files" />
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133
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134 <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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135 <option value="" selected="true">Consensus</option>
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136 <option value="--polymorphism-prediction">Polymorphism</option>
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137 </param>
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138
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139 <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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140
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141 <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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142
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143 <section name="output_options" title="Output Options" expanded="false">
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144 <param name="formats" type="select" multiple="true" optional="false" display="checkboxes" label="Output Formats">
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145 <option value="gd" selected="true">Variants (GenomeDiff)</option>
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146 <option value="html">Variant Report (Webpage)</option>
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147 <option value="zip">All Variant Results (Gzip)</option>
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148 <option value="log">Log (Text)</option>
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149 </param>
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150 </section>
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151
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152 </when>
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153 <when value="annotate">
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154
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155 <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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156
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157 <expand macro="annotate_format_opts">
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158 <option value="gd" selected="true">Annotated Variants (GenomeDiff)</option>
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159 </expand>
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160
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161 </when>
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162 <when value="compare">
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163
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164 <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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165
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166 <expand macro="annotate_format_opts">
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167 <option value="phylip" selected="true">Variant Comparison (Phylip)</option>
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168 <option value="gd">Annotated Variants (GenomeDiff)</option>
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169 </expand>
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170
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171 </when>
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172 </conditional>
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173
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174 </inputs>
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175
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176 <outputs>
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177 <data format="html" name="report" label="${tool.name} on ${on_string}: Variants (Webpage)">
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178 <filter>run['mode'] == 'detect' and 'html' in run['output_options']['formats']</filter>
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179 </data>
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180 <data format="html" name="annreport" label="${tool.name} on ${on_string}: Annotated Variants Report (Webpage)">
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181 <filter>run['mode'] != 'detect' and 'html' in run['output_options']['formats']</filter>
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182 </data>
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183
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184 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Variants (GenomeDiff)">
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185 <filter>run['mode'] == 'detect' and 'gd' in run['output_options']['formats']</filter>
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186 </data>
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187 <data format="tabular" name="genomediff" label="${tool.name} on ${on_string}: Annotated Variants (GenomeDiff)">
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188 <filter>run['mode'] != 'detect' and 'gd' in run['output_options']['formats']</filter>
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189 </data>
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190
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191 <data format="zip" name="zip_output" label="${tool.name} on ${on_string}: All Variant Results (Gzip)">
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192 <filter>'zip' in run['output_options']['formats']</filter>
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193 </data>
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194 <data format="txt" name="log" label="${tool.name} on ${on_string}: Breseq Log">
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195 <filter>'log' in run['output_options']['formats']</filter>
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196 </data>
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197 <data format="tabular" name="tabdelim" label="${tool.name} on ${on_string}: Annotated Variants (Tabular)">
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198 <filter>'tsv' in run['output_options']['formats']</filter>
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199 </data>
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200 <data format="phylip" name="phylipout" label="${tool.name} on ${on_string}: Variant Comparison (Phylip)">
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201 <filter>'phylip' in run['output_options']['formats']</filter>
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202 </data>
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203 <data format="txt" name="jsonout" label="${tool.name} on ${on_string}: Annotated Variants (JSON)">
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204 <filter>'json' in run['output_options']['formats']</filter>
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205 </data>
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206 </outputs>
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207
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208 <tests>
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209 <test>
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210 <repeat name="references">
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211 <conditional name="reference">
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212 <param name="source" value="history" />
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213 <param name="own_genome" value="lambda.gbk" />
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214 </conditional>
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215 </repeat>
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216 <conditional name="run">
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217 <param name="mode" value="detect" />
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218 <param name="fastqs" value="lambda.short_sequence_repeats.fastq" />
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219 <param name="polymorphism_prediction" value="" />
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220 <param name="name" value="smallest" />
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221 <param name="predict_junctions" value="" />
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222 <section name="output_options">
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223 <param name="formats" value="html,log,gd,zip" />
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224 </section>
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225 </conditional>
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226
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227 <output name="report" file="report.html" compare="sim_size" delta="100" />
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228 <output name="log" file="log.txt" lines_diff="4">
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229 <assert_contents>
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230 <has_text text="breseq --num-processors" />
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231 </assert_contents>
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232 </output>
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233 <output name="output" file="gdout.txt" lines_diff="8" />
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234 <output name="zip_output">
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235 <assert_contents>
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236 <has_archive_member path="results/output/output.gd" />
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237 </assert_contents>
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238 </output>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
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239 </test>
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240 <test>
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241 <repeat name="references">
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242 <conditional name="reference">
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243 <param name="source" value="builtin" />
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244 <param name="fixed_genome" value="lambda1" />
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245 </conditional>
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246 </repeat>
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247 <conditional name="run">
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248 <param name="mode" value="detect" />
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249 <param name="fastqs" value="lambda.short_sequence_repeats.fastq" />
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250 <param name="polymorphism_prediction" value="" />
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251 <param name="name" value="smallest" />
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252 <param name="predict_junctions" value="" />
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253 <section name="output_options">
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254 <param name="formats" value="gd" />
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255 </section>
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256 </conditional>
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257
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258 <output name="output" file="gdout.txt" lines_diff="8" />
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259 </test>
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260 <test>
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261 <repeat name="references">
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262 <conditional name="reference">
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263 <param name="source" value="history" />
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264 <param name="own_genome" value="lambda.gbk" />
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265 </conditional>
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266 </repeat>
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267 <conditional name="run">
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268 <param name="mode" value="annotate" />
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269 <param name="gds" value="gdout.txt" />
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270 <section name="output_options">
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271 <param name="formats" value="html" />
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272 </section>
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273 </conditional>
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274
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275 <output name="annreport" file="gdtoolsout.html" compare="sim_size" delta="100" />
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276 </test>
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277 </tests>
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278
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279 <help>
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280 <![CDATA[
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281 **Detect Variants**
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282
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283 breseq (pronounced: \\brēz-ˈsēk\\ or breeze-seq) is a computational pipeline for
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284 the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent,
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285 etc.). It uses reference-based alignment approaches to predict mutations in a
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286 sample relative to an already sequenced genome. breseq is intended for microbial
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287 genomes (<10 Mb) and re-sequenced samples that are only slightly diverged from
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288 the reference sequence (<1 mutation per 1000 bp).
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289
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290 breseq's primary advantages over other software programs are that it can:
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291
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292 - Accurately predict new sequence junctions, such as those associated with mobile element insertions.
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293 - Integrate multiple sources of evidence for genetic changes into mutation predictions.
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294 - Produce annotated output describing biologically relevant mutational events.
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295
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296 breseq was initially developed to analyze data from the Lenski long-term
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297 evolution experiment with `E. coli`_. References: barrick2009a_ barrick2009b_.
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298
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299 .. _`E. coli`: http://myxo.css.msu.edu/ecoli/
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300 .. _barrick2009a: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009a
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301 .. _barrick2009b: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009b
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302
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303 However, breseq may be generally useful to researchers who are:
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304
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305 - Tracking mutations over time in microbial evolution experiments.
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306 - Checking strains for unwanted second-site mutations after genetic manipulations.
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307 - Identifying mutations that occur during strain improvement or after long-term culture of engineered strains.
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308 - Discovering what mutations arise in pathogens during infection or cause antibiotic resistance.
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309
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310
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311 *Inputs*
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312
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313 Breseq accepts files in FASTQ format. It does not take pair-end information into
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314 account.
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315
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316 You can either run in clonal (consensus) mode or search for polymorphisms in a
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317 population.
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318
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319 You can also select an external sequence (eg. a transposon) to detect for
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320 insertions or horizontal transfer.
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321
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322
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323 *Outputs*
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324
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325 Breseq outputs a number of files. These are all condensed in a single zipped
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326 file.
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327
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328 It contains output files with the final results, accessible through
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329 ``output/index.html``
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330
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331 It also contains data files with accessory data, including:
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332
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333 - ``data/reference.fasta`` (file with reference genome: can be used in eg. IGV browser)
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334 - ``data/reference.gff`` (file with genomic annotations: can be used in eg. IGV browser)
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335 - ``data/areference.bam`` (file with read alignments: can be used in eg. IGV browser)
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336 - ``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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337
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338
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339 ----
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340
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341 **Annotate Variants**
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342
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343 Annotate a GenomeDiff file (generated by breseq) with information about
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344 mutations (what genes they affect, amino acid substitutions, etc.) If multiple
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345 input files are provided, then also COMPARE the frequencies for identical
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346 mutations across samples.
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347 ]]>
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348 </help>
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349
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350 <citations>
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351 <citation type="doi">10.1007/978-1-4939-0554-6_12</citation>
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352 </citations>
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353
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354 </tool>