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1 <tool id="vsnp_determine_ref_from_data" name="vSNP: determine reference" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@">
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2 <description>from input data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="biopython_requirement"/>
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8 <expand macro="pyyaml_requirement"/>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 #set gzipped = 'false'
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13 #set input_type = $input_type_cond.input_type
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14
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15 #if $input_type in ["single", "pair"]:
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16 #set read1 = $input_type_cond.read1
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17 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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18 ln -s '${read1}' '${read1_identifier}' &&
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19 #if $input_type == "pair":
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20 #set read2 = $input_type_cond.read2
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21 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
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22 ln -s '${read2}' '${read2_identifier}' &&
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23 #else:
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24 #set read2 = None
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25 #end if
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26 #else:
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27 #set read1 = $input_type_cond.reads_collection['forward']
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28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
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29 ln -s '${read1}' '${read1_identifier}' &&
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30 #set read2 = $input_type_cond.reads_collection['reverse']
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31 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
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32 ln -s '${read2}' '${read2_identifier}' &&
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33 #end if
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34
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35 python '$__tool_directory__/vsnp_determine_ref_from_data.py'
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36 --read1 '${read1_identifier}'
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37 #if $read2 is not None
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38 --read2 '${read2_identifier}'
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39 #end if
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40 --output_dbkey '$output_dbkey'
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41 --output_metrics '$output_metrics'
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42 #if $read1.is_of_type('fastqsanger.gz'):
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43 --gzipped
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44 #end if
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45 #set $dnaprint_fields = $__app__.tool_data_tables['vsnp_dnaprints'].get_fields()
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46 #for $i in $dnaprint_fields:
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47 --dnaprint_fields '${i[0]}' '${i[2]}'
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48 #end for
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49 ]]></command>
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50 <inputs>
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51 <conditional name="input_type_cond">
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52 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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53 <option value="single" selected="true">Single files</option>
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54 <option value="paired">Paired reads</option>
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55 <option value="pair">Paired reads in separate data sets</option>
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56 </param>
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57 <when value="single">
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58 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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59 </when>
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60 <when value="paired">
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61 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
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62 </when>
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63 <when value="pair">
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64 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
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65 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data name="output_dbkey" format="txt" label="${tool.name} on ${on_string} (dbkey)"/>
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71 <data name="output_metrics" format="txt" label="${tool.name} on ${on_string} (metrics)"/>
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72 </outputs>
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73 <tests>
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74 <!-- 1 single read -->
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75 <test expect_num_outputs="2">
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76 <param name="input_type" value="single"/>
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77 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz"/>
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78 <output name="output_dbkey" file="output_dbkey.txt" ftype="txt"/>
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79 <output name="output_metrics" file="output_metrics.txt" ftype="txt"/>
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80 </test>
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81 <!-- 1 set of paired reads -->
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82 <test expect_num_outputs="2">
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83 <param name="input_type" value="pair"/>
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84 <param name="read1" value="CMC_20E1_R1.fastq.gz" ftype="fastqsanger.gz"/>
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85 <param name="read2" value="CMC_20E1_R2.fastq.gz" ftype="fastqsanger.gz"/>
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86 <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/>
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87 <output name="output_metrics" file="paired_metrics.txt" ftype="txt"/>
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88 </test>
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89 <!-- A collection of paired reads -->
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90 <test expect_num_outputs="2">
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91 <param name="input_type" value="paired"/>
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92 <param name="reads_collection">
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93 <collection type="paired">
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94 <element name="forward" value="CMC_20E1_R1.fastq.gz" ftype="fastqsanger.gz"/>
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95 <element name="reverse" value="CMC_20E1_R2.fastq.gz" ftype="fastqsanger.gz"/>
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96 </collection>
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97 </param>
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98 <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/>
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99 <output name="output_metrics" file="paired_collection_metrics.txt" ftype="txt"/>
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100 </test>
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101 </tests>
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102 <help>
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103 **What it does**
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104
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105 Accepts a single fastqsanger read, a set of paired reads, or a collection of single or paired reads (bacterial samples) and
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106 inspects the data to discover the best reference genome for aligning the reads.
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107
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108 The information needed to discover the best reference is maintained by the USDA in this repository_. References are curreently
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109
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110 .. _repository: https://github.com/USDA-VS/vSNP_reference_options
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111
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112 limited to TB complex, paraTB, and Brucella, but information for additional references will be added. The information for each
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113 reference is a string consisting of zeros and ones, compiled by USDA researchers, which we call a "DNA print". These strings
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114 are maintained in yaml files for use in Galaxy, and are installed via the **vSNP DNAprints data manager** tool.
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115
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116 This tool creates an in-memory dictionary of these DNA print strings for matching with a string generated by inspecting the
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117 input sample data. During inspection, this tool accrues sequence counts for supported species, ultimately generating a string
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118 consisting of zeros and ones based on the counts, (i.e., a DNA print). This string is then compared to the strings contained
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119 in the in-memory dictionary of DNA prints to find a match.
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120
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121 The strings in the in-memory dictionary are each associated with a Galaxy "dbkey" (i.e., genome build), so when a match is found,
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122 the associated "dbkey" is passed to a mapper (e.g., **Map with BWA-MEM**), typically within a workflow via an expression tool,
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123 to align the reads to the associated reference.
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124
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125 This tool produces 2 text files, a "dbkey" file that contains the dbkey string and a "metrics" file that provides information
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126 about the sequence counts that were discovered in the input sample data that produced the "DNA print" string.
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127
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128 This tool is important for samples containing bacterial species because many of the samples have a "mixed bag" of species,
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129 and discovering the primary species is critical. DNA print matching is currently supported for the following genomes.
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130
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131 * Mycobacterium bovis AF2122/97
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132 * Brucella abortus bv. 1 str. 9-941
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133 * Brucella abortus strain BER
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134 * Brucella canis ATCC 23365
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135 * Brucella ceti TE10759-12
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136 * Brucella melitensis bv. 1 str. 16M
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137 * Brucella melitensis bv. 3 str. Ether
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138 * Brucella melitensis BwIM_SOM_36b
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139 * Brucella melitensis ATCC 23457
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140 * Brucella ovis ATCC 25840
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141 * Brucella suis 1330
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142 * Mycobacterium tuberculosis H37Rv
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143 * Mycobacterium avium subsp. paratuberculosis strain Telford
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144 * Mycobacterium avium subsp. paratuberculosis K-10
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145 * Brucella suis ATCC 23445
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146 * Brucella suis bv. 3 str. 686
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147
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148 **Required Options**
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149
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150 * **Choose the category of the files to be analyzed** - select "Single files" or "Collection of files", then select the appropriate history items (single or paired fastqsanger reads or a collection of fastqsanger reads) based on the selected option.
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151 </help>
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152 <expand macro="citations"/>
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153 </tool>
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