annotate staramr_search.xml @ 3:9047a1d3d8ea draft

planemo upload for repository https://github.com/phac-nml/staramr commit 679a3b6784cfbca8f3623d316d6101672b4a5531
author nml
date Tue, 14 Aug 2018 10:04:19 -0400
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children 1e8ec0f861ff
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1 <tool id="staramr_search" name="staramr" version="0.2.2">
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2 <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
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3 <requirements>
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4 <requirement type="package" version="0.2.2">staramr</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #import re
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8
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9 #set $named_genomes = ''
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10 #for $genome in $genomes
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11 #set $_named_genome = re.sub(r'(\s|\(|\))', '_', '"{}.fasta"'.format($genome.element_identifier))
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12 ln -s "$genome" $_named_genome &&
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13 #set $named_genomes = $named_genomes + ' ' + $_named_genome
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14 #end for
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16 #set $excel_proper_extension = '"{}.xlsx"'.format($excel)
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17 ln -s "$excel" $excel_proper_extension &&
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19 staramr search
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21 --nprocs "\${GALAXY_SLOTS:-1}"
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23 --pid-threshold $advanced.pid_threshold
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24 --percent-length-overlap-resfinder $advanced.plength_resfinder
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25 --percent-length-overlap-pointfinder $advanced.plength_pointfinder
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27 $advanced.report_all_blast
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28 $advanced.exclude_negatives
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29 $advanced.exclude_resistance_phenotypes
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31 --output-summary $summary
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32 --output-resfinder $resfinder
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33 #if $use_pointfinder.enable
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34 --output-pointfinder $pointfinder
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35 #end if
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36 --output-settings $settings
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37 --output-excel $excel_proper_extension
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38
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39 --output-hits-dir staramr_hits
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41 #if $use_pointfinder.enable
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42 --pointfinder-organism $use_pointfinder.organism
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43 #end if
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45 $named_genomes
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46 ]]></command>
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47 <inputs>
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48 <param type="data" name="genomes" format="fasta" multiple="true"/>
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49 <conditional name="use_pointfinder">
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50 <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" />
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51 <when value="true">
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52 <param name="organism" type="select" label="Select a pointfinder organism">
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53 <option value="salmonella" selected="true">Salmonella</option>
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54 </param>
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55 </when>
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56 <when value="false" />
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57 </conditional>
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58 <section name="advanced" title="Advanced options" expanded="false">
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59 <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0"
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60 min="0" max="100" help="(--pid-threshold)" />
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61 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
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62 min="0" max="100" help="(--percent-length-overlap-resfinder)" />
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63 <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0"
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64 min="0" max="100" help="(--percent-length-overlap-pointfinder)" />
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65 <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue=""
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66 help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
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67 <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
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68 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
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69 </section>
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70 </inputs>
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71 <outputs>
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72 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
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73 <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
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74 <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv">
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75 <filter>use_pointfinder['enable']</filter>
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76 </data>
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77 <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" />
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78 <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" />
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79 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
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80 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
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81 </collection>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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86 <conditional name="use_pointfinder">
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87 <param name="enable" value="true" />
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88 <param name="organism" value="salmonella" />
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89 </conditional>
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90
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91 <output name="summary" file="test1-summary.tsv" ftype="tabular" />
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92 <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
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93 <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
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94 <output_collection name="blast_hits" type="list">
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95 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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96 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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97 </output_collection>
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98 </test>
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99 <test>
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100 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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101
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102 <output name="summary" file="test2-summary.tsv" ftype="tabular" />
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103 <output name="resfinder" file="test2-resfinder.tsv" ftype="tabular" />
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104 <output_collection name="blast_hits" type="list">
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105 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
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106 </output_collection>
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107 </test>
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108 <test>
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109 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
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110 <param name="pid_threshold" value="99.8" />
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111
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112 <output name="summary" file="test3-summary.tsv" ftype="tabular" />
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113 </test>
1
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114 <test>
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115 <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" />
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116 <param name="pid_threshold" value="99.8" />
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117
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118 <output name="summary" file="test4-summary.tsv" ftype="tabular" />
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119 </test>
0
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120 </tests>
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121 <help><![CDATA[
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122 staramr
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123 =======
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124
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125 staramr_ scans bacterial genome contigs against both the ResFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
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126
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127 Usage
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128 -----
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129
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130 1. Select your genome contigs (in FASTA format).
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131 2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported).
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132 3. Run the tool.
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133
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134 Output
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135 ------
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136
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137 There are 5 different output files produced by `staramr` as well as a collection of additional files.
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138
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139 summary.tsv
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140 ```````````
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141
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142 A summary of all detected AMR genes/mutations in each genome, one genome per line.
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143
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144 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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145 | Isolate ID | Genotype | Predicted Phenotype |
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146 +============+===========================================================+===========================================================================================================+
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147 | SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline |
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148 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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149 | SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline |
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150 +------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
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151
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152 resfinder.tsv
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153 `````````````
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154
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155 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
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156
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157 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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158 | Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession |
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159 +============+============+======================+============+===========+==========================+==============+========+=======+===========+
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160 | SRR1952908 | sul3 | sulfisoxazole | 100.00 | 100.00 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 |
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161 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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162 | SRR1952908 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00032 | 1551 | 2750 | AJ517790 |
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163 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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164 | SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100.00 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 |
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165 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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166 | SRR1952908 | aadA1 | streptomycin | 100.00 | 100.00 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 |
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167 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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168 | SRR1952908 | aadA2 | streptomycin | 99.75 | 100.00 | 792/792 | contig00030 | 7760 | 6969 | JQ364967 |
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169 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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170 | SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 |
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171 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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172 | SRR1952926 | tet(A) | tetracycline | 99.92 | 100.00 | 1200/1200 | contig00027 | 1480 | 2679 | AJ517790 |
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173 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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174 | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 |
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175 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
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176
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177 pointfinder.tsv
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178 ```````````````
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179
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180 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
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181
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182 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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183 | Isolate ID | Gene | Predicted Phenotype | Type | Position | Mutation | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End |
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184 +=============+==============+====================================+========+===========+======================+============+===========+==========================+==============+=========+========+
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185 | SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00008 | 22801 | 20165 |
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186 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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187 | SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | codon | 83 | TCC -> TAC (S -> Y) | 99.96 | 100.00 | 2637/2637 | contig00011 | 157768 | 160404 |
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188 +-------------+--------------+------------------------------------+--------+-----------+----------------------+------------+-----------+--------------------------+--------------+---------+--------+
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189
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190 settings.txt
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191 ````````````
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192
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193 The command-line, database versions, and other settings used to run `staramr`.
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194
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195 ::
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196
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197 command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
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198 version = 0.2.0
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199 start_time = 2018-06-05 14:41:44
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200 end_time = 2018-06-05 14:41:47
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201 total_minutes = 0.05
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202 resfinder_db_dir = staramr/databases/data/dist/resfinder
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203 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
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204 resfinder_db_commit = dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2
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205 resfinder_db_date = Tue, 20 Mar 2018 16:49
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206 pointfinder_db_dir = staramr/databases/data/dist/pointfinder
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207 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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208 pointfinder_db_commit = ba65c4d175decdc841a0bef9f9be1c1589c0070a
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209 pointfinder_db_date = Fri, 06 Apr 2018 09:02
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210 pointfinder_gene_drug_version = 050218
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211 resfinder_gene_drug_version = 050218
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212
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213 results.xlsx
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214 ````````````
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215
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216 An Excel spreadsheet containing the previous 4 files as separate worksheets.
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217
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218 BLAST Hits
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219 ``````````
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220
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221 The dataset collection **hits** stores fasta files of the specific blast hits.
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222
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223 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
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224
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225 .. _staramr: https://github.com/phac-nml/staramr
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226 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
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227 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
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228 .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/
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229 ]]></help>
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230 <citations>
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231 <citation type="bibtex">
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232 @misc{githubstaramr,
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233 author = {Petkau, Aaron},
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234 year = {2018},
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235 title = {staramr},
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236 publisher = {GitHub},
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237 journal = {GitHub repository},
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238 url = {https://github.com/phac-nml/staramr},
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239 }</citation>
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240 </citations>
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241 </tool>