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1 <tool id="breseq" name="Breseq Variant Report" version="0.31.1" hidden="false">
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2 <description>Runs Breseq software on a set of fastq files</description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.31.1">breseq</requirement>
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6 </requirements>
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7
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8 <command interpreter="python">
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9 breseq_wrapper.py
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10
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11 $outfile
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12 $outfile.files_path
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13
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14 --num-processors \${GALAXY_SLOTS:-4}
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15
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16 #if str($reference.source) == "history":
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17 #for $i, $s in enumerate( $reference.ref_series )
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18 -r $s.own_genome
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19 #end for
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20 #else:
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21 -r $reference.fixed_genome.fields.path
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22 #end if
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23 #for $i, $s in enumerate( $read_series )
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24 ${s.input}
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25 #end for
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26
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27 #if str($polymorphism.selection) == "yes":
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28 --polymorphism-prediction
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29 --polymorphism-reject-indel-homopolymer-length $polymorphism.indel_homopolymer_length
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30 --polymorphism-reject-surrounding-homopolymer-length $polymorphism.surrounding_homopolymer_length
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31 --polymorphism-minimum-coverage-each-strand $polymorphism.strand_coverage
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32 --polymorphism-bias-cutoff $polymorphism.bias_pvalue
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33 #end if
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34
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35 #if str($junction_reference.selection) == "yes":
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36 #for $i, $s in enumerate( $junction_reference.j_series )
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37 --junction-only-reference $s.jc_genome
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38 #end for
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39 #end if
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40
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41 ${cnv_evidence}
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42
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43 -b $minqvalue
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44
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45 </command>
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46
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47 <stdio>
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48 <exit_code range="1:" level="fatal" description="Fatal ERROR exit code greater than 1" />
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49 </stdio>
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50
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51 <inputs>
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52 <!-- reference genome -->
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53 <conditional name="reference">
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54 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in genome?" >
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55 <option value="indexed">Use a built-in genome</option>
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56 <option value="history">Use one from the history</option>
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57 </param>
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58 <when value="indexed">
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59 <param name="fixed_genome" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Bioinformatics team">
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60 <options from_data_table="genbank_files">
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61 <filter type="sort_by" column="2"/>
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62 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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63 </options>
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64 </param>
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65 </when>
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66 <when value="history">
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67 <!-- <param name="own_genome" type="data" label="Select the reference genome (fasta or genbank)" /> -->
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68 <repeat name="ref_series" title="Reference Genome" min="1">
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69 <param name="own_genome" type="data" label="Select the reference genome (fasta or genbank)" />
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70 </repeat>
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71 </when>
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72 </conditional>
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73
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74
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75 <!-- input Fastq files -->
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76 <repeat name="read_series" title="Read File" min="1">
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77 <param name="input" type="data" format="fastq" label="Dataset" />
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78 </repeat>
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79
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80
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81 <!-- select polymorphism -->
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82 <conditional name="polymorphism">
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83 <param name="selection" type="select" label="Perform polimorphism detection" help="Do you want to perform polimorphism detection in a population">
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84 <option value="no">Do not perform polymorphism detection</option>
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85 <option value="yes">Perform polymorphism detection</option>
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86 </param>
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87 <when value="yes">
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88 <param name="indel_homopolymer_length" type="integer" value="0" label="Reject insertion/deletion polymorphisms due to homopolymer repeats with this length or greater" />
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89 <param name="surrounding_homopolymer_length" type="integer" value="0" label="Do not predict polymorphic base substitutions that create a homopolymer with this length on each side (with 2 TTATT->TTTTT is rejected)" />
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90 <param name="strand_coverage" type="integer" value="3" label="Only accept polymorphisms if coverage in each strand is at least this" />
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91 <param name="bias_pvalue" type="float" value="0.05" label="Only accept polymorphisms if pvalue of strand or read quality bias is greater than this" />
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92 </when>
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93 <when value="no" />
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94 </conditional>
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95
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96 <!-- junction only reference(s) -->
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97 <conditional name="junction_reference">
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98 <param name="selection" type="select" label="Detect external sequence insertion" help="You can select external sequences to detect insertions">
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99 <option value="no">Do not detect external sequence insertion</option>
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100 <option value="yes">Detect external sequence insertions</option>
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101 </param>
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102 <when value="yes">
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103 <repeat name="j_series" title="Junction-only references" min="1">
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104 <param name="jc_genome" type="data" label="Select an external sequence (fasta or genbank)" />
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105 </repeat>
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106 </when>
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107 <when value="no" />
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108 </conditional>
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109
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110 <!-- Copy Number Evidence -->
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111 <param name="cnv_evidence" type="select" label="Copy number variation prediction (experimental option)" help="Do you want to perform copy number variation prediction">
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112 <option value="">Do not perform copy number variaion prediction</option>
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113 <option value="--cnv">Perform copy number variation prediction (--cnv)</option>
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114 </param>
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115
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116 <param name="minqvalue" type="integer" value="3" label="Minimum Phred Q for a base to be considered" />
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117
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118
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119 </inputs>
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120
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121 <outputs>
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122 <data format="prezip.html" name="outfile" label="Breseq HTML report" />
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123 </outputs>
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124
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125 <help>
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126 **Breseq**
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127
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128 Breseq_ is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes.
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129
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130 .. _Breseq: http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing
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131
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132 ------
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133
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134 **Inputs**
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135
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136 Breseq accepts files in FASTQ format. It does not take pair-end information into account.
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137
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138 You can either run in clonal (consensus) mode or search for polymorphisms in a population.
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139
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140 You can also select an external sequence (eg. a transposon) to detect for insertions or horizontal transfer.
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141
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142
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143 ------
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144
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145 **Outputs**
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146
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147 Breseq outputs a number of files. These are all condensed in a single zipped file.
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148
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149 It contains output files with the final results, accessible through ``output/index.html``
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150
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151 It also contains data files with accessory data, including:
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152
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153 - ``data/reference.fasta`` (file with reference genome: can be used in eg. IGV browser)
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154 - ``data/reference.gff`` (file with genomic annotations: can be used in eg. IGV browser)
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155 - ``data/areference.bam`` (file with read alignments: can be used in eg. IGV browser)
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156 - ``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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157
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158 </help>
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159 </tool>
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160
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