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planemo upload for repository https://github.com/phac-nml/bio_hansel commit a7add3a4ffc9275f78d4583aac1ef3281c0def21
author nml
date Wed, 09 May 2018 15:06:32 -0400
parents e9fd173fc7ee
children
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8:e9fd173fc7ee 9:4654c51dae72
1 <tool id="bio_hansel" name="Bio Hansel" version="1.3.1"> 1 <tool id="bio_hansel" name="bio_hansel" version="2.0.0">
2 <description>SNV Subtyping with genome assemblies or reads</description> 2 <description>SNV subtyping of genome sequence reads or assemblies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.1">bio_hansel</requirement> 4 <requirement type="package" version="2.0.0">bio_hansel</requirement>
5 <requirement type="package" version="17.2.0">attrs</requirement> 5 </requirements>
6 </requirements> 6 <command detect_errors="exit_code">
7 <command detect_errors="exit_code"><![CDATA[ 7 <![CDATA[
8 ## Preparing file input. 8
9 #if $data_type.type == "paired": 9 #import re
10 10
11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq && 11 #def is_gzipped_fastq($data_input)
12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name'.fastq && 12 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
13 13 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
14 #elif $data_type.type == "collection": 14 #end def
15 15
16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && 16 #def get_fastq_ext($data_input)
17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && 17 ## Get file extension for FASTQ data param
18 18 #return '.fastq.gz' if $is_gzipped_fastq($data_input) else '.fastq'
19 #elif $data_type.type == "single": 19 #end def
20 20
21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): 21 #def base_sample_name($name)
22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq && 22 #if $re.search(r'_R(1|2)', $name):
23 #end if 23 #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name)
24 24 #elif $re.match(r'.+_\d\.', $name):
25 #if $data_type.fastq_input1.is_of_type('fasta'): 25 #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name)
26 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fasta && 26 #else
27 #end if 27 #return $name
28 28 #end if
29 #end if 29 #end def
30 30
31 31 #def get_paired_fastq_filename($data_input, $name=None, $is_forward=True)
32 ## Checking for custom scheme. 32 ## Get paired FASTQ filename for a data param with appropriate file extension
33 #if $type_of_scheme.scheme_type == "custom": 33 ## with '_1' or '_2' appended if forward or reverse reads, respectively.
34 #if $type_of_scheme.scheme_input.is_of_type('fasta'): 34 #set $name = $name if $name is not None else $data_input.name
35 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' && 35 #set $name = $base_sample_name($name)
36 #end if 36 #set $postfix = '1' if $is_forward else '2'
37 #end if 37 #set $ending = '_{}{}'.format($postfix, $get_fastq_ext($data_input))
38 38 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending)
39 ## Start the actual command here 39 #end def
40 hansel 40
41 41 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz)
42 42 #if $input.type == 'fasta'
43 ## Select the scheme 43 #set $input_files = '"{}"'.format($input.fasta.name)
44 -s 44 ln -s "$input.fasta" $input_files &&
45 45 #elif $input.type == 'paired'
46 #if $type_of_scheme.scheme_type == "heidelberg": 46 #set $forward_filename = $get_paired_fastq_filename($input.forward)
47 heidelberg 47 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)
48 #elif $type_of_scheme.scheme_type == "enteritidis": 48 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
49 enteritidis 49 ln -s "$input.forward" $forward_filename &&
50 #elif $type_of_scheme.scheme_type == "custom": 50 ln -s "$input.reverse" $reverse_filename &&
51 '$type_of_scheme.scheme_input.name' 51 #elif $input.type == 'single'
52 #end if 52 #set $input_files = '"{}"'.format($input.single.name)
53 53 ln -s "$input.single" $input_files &&
54 ## Use Json output 54 #elif $input.type == 'paired_collection'
55 #if $dev_args.use_json == "yes": 55 #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward, $input.paired_collection.name)
56 --json 56 #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, $input.paired_collection.name, is_forward=False)
57 #end if 57 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
58 58 ln -s "$input.paired_collection.forward" $forward_filename &&
59 #if $kmer_vals.kmer_min 59 ln -s "$input.paired_collection.reverse" $reverse_filename &&
60 --min-kmer-freq $kmer_vals.kmer_min 60 #end if
61 #end if 61
62 62 ## Checking for custom scheme.
63 #if $kmer_vals.kmer_max 63 #if $type_of_scheme.scheme_type == "custom":
64 --max-kmer-freq $kmer_vals.kmer_max 64 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
65 #end if 65 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
66 66 #end if
67 #if $qc_vals.low_cov_depth_freq 67 #end if
68 --low-cov-depth-freq $qc_vals.low_cov_depth_freq 68
69 #end if 69 hansel
70 70 -vvv
71 #if $qc_vals.max_missing_tiles 71 -t "\${GALAXY_SLOTS:-1}"
72 --max-missing-tiles $qc_vals.max_missing_tiles 72 -o results.tab
73 #end if 73 -O match_results.tab
74 74 -S tech_results.tab
75 #if $qc_vals.min_ambiguous_tiles 75 $dev_args.use_json
76 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles 76 $input_files
77 #end if 77 --scheme
78 78 #if $type_of_scheme.scheme_type == "custom":
79 #if $qc_vals.max_intermediate_tiles 79 '$type_of_scheme.scheme_input.name'
80 --max-intermediate-tiles $qc_vals.max_intermediate_tiles 80 #else:
81 #end if 81 $type_of_scheme.scheme_type
82 82 #end if
83 #if $qc_vals.low_coverage_warning 83 #if $kmer_vals.kmer_min
84 --low-cov-warning $qc_vals.low_coverage_warning 84 --min-kmer-freq $kmer_vals.kmer_min
85 #end if 85 #end if
86 86 #if $kmer_vals.kmer_max
87 ## Adding more parameters to the command. 87 --max-kmer-freq $kmer_vals.kmer_max
88 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab 88 #end if
89 89 #if $qc_vals.low_cov_depth_freq
90 90 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
91 ## Entering the file inputs 91 #end if
92 92 #if $qc_vals.max_missing_tiles
93 #if $data_type.type == "single": 93 --max-missing-tiles $qc_vals.max_missing_tiles
94 94 #end if
95 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): 95 #if $qc_vals.min_ambiguous_tiles
96 '$data_type.fastq_input1.name'.fastq 96 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
97 #end if 97 #end if
98 98 #if $qc_vals.max_intermediate_tiles
99 #if $data_type.fastq_input1.is_of_type('fasta'): 99 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
100 '$data_type.fastq_input1.name'.fasta 100 #end if
101 #end if 101 #if $qc_vals.low_coverage_warning
102 102 --low-cov-warning $qc_vals.low_coverage_warning
103 #elif $data_type.type =="collection": 103 #end if
104 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq 104 ]]>
105 105 </command>
106 #elif $data_type.type =="paired": 106 <inputs>
107 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq 107 <conditional name="input">
108 #end if 108 <param name="type" type="select" label="Sequence input type">
109 109 <option value="fasta">FASTA</option>
110 ]]></command> 110 <option value="paired">Paired-end FASTQs</option>
111 <inputs> 111 <option value="single">Single-end FASTQ</option>
112 <conditional name="data_type"> 112 <option value="paired_collection">Paired-end FASTQ collection</option>
113 <param name="type" type="select" label="Specify the read type."> 113 </param>
114 <option value="single">Single-end Data</option> 114 <when value="fasta">
115 <option value="paired">Paired-end Data</option> 115 <param name="fasta"
116 <option value="collection">Collection Paired-end Data</option> 116 type="data" format="fasta"
117 </param> 117 optional="false"
118 <when value="single"> 118 label="FASTA file"
119 <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/> 119 />
120 </when> 120 </when>
121 <when value="paired"> 121 <when value="paired">
122 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/> 122 <param name="forward"
123 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/> 123 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
124 </when> 124 optional="false"
125 <when value="collection"> 125 label="Forward FASTQ file"
126 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> 126 help="Must have ASCII encoded quality scores"
127 </when> 127 />
128 </conditional> 128 <param name="reverse"
129 <conditional name="type_of_scheme"> 129 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
130 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)"> 130 optional="false"
131 <option value="heidelberg">Heidelberg scheme</option> 131 label="Reverse FASTQ file"
132 <option value="enteritidis">Enteritidis scheme</option> 132 help="File format must match the Forward FASTQ file"
133 <option value="custom">Specify your own custom scheme</option> 133 />
134 </param> 134 </when>
135 <when value="heidelberg"/> 135 <when value="single">
136 <when value="enteritidis"/> 136 <param name="single"
137 <when value="custom"> 137 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
138 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/> 138 optional="false"
139 </when> 139 label="Single-end FASTQ file"
140 </conditional> 140 />
141 <!-- K-mer frequencies. --> 141 </when>
142 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False"> 142 <when value="paired_collection">
143 <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" value="8" help="default = 8"/> 143 <param name="paired_collection"
144 <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" value="1000" help="default = 1000"/> 144 type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,txt"
145 </section> 145 collection_type="paired"
146 <!-- Quality Checking Parameters --> 146 optional="false"
147 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False"> 147 label="Paired-end FASTQ collection"
148 <param name="low_cov_depth_freq" argument="--low-cov-depth-freq" optional="True" type="integer" min="0" label="QC: Frequency below this coverage are considered low coverage" value="20" help="default = 20"/> 148 help=""
149 <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/> 149 />
150 <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> 150 </when>
151 <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> 151 </conditional>
152 <param name="low_coverage_warning" argument="--low-cov-warning" optional="True" type="integer" min="0" label="QC: Overall tile coverage below this value will trigger a low coverage warning" value="20" help="default = 20"/> 152 <conditional name="type_of_scheme">
153 </section> 153 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">
154 <section name="dev_args" title="Developer Options" expanded="False"> 154 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
155 <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details"> 155 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
156 <option value="no">no</option> 156 <option value="custom">Specify your own custom scheme</option>
157 <option value="yes">yes</option> 157 </param>
158 </param> 158 <when value="heidelberg"/>
159 </section> 159 <when value="enteritidis"/>
160 </inputs> 160 <when value="custom">
161 <outputs> 161 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/>
162 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> 162 </when>
163 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> 163 </conditional>
164 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> 164 <!-- K-mer frequencies. -->
165 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> 165 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
166 <filter>dev_args['use_json'] == "yes"</filter> 166 <param name="kmer_min" type="integer"
167 </data> 167 argument="--min-kmer-freq"
168 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> 168 optional="true"
169 <filter>dev_args['use_json'] == "yes"</filter> 169 min="0" value="8"
170 </data> 170 label="Min k-mer frequency/coverage"
171 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> 171 help="default = 8"/>
172 <filter>dev_args['use_json'] == "yes"</filter> 172 <param name="kmer_max" type="integer"
173 </data> 173 argument="--max-kmer-freq"
174 </outputs> 174 optional="true"
175 <tests> 175 min="1" value="1000"
176 <test> 176 label="Max k-mer frequency/coverage"
177 <param name="type" value="single"/> 177 help="default = 1000"/>
178 <param name="type_of_scheme" value="heidelberg"/> 178 </section>
179 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/> 179 <!-- Quality Checking Parameters -->
180 <output name="results.tab"> 180 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
181 <assert_contents> 181 <param name="low_cov_depth_freq" type="integer"
182 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/> 182 argument="--low-cov-depth-freq"
183 </assert_contents> 183 value="20" min="0"
184 </output> 184 optional="true"
185 <output name="match_results.tab"> 185 label="QC: Frequency below this coverage are considered low coverage"
186 <assert_contents> 186 help="default = 20"/>
187 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> 187 <param name="min_ambiguous_tiles" type="integer"
188 </assert_contents> 188 argument="--min-ambiguous-tiles"
189 </output> 189 optional="true"
190 <output name="tech_results.tab"> 190 value="3" min="0"
191 <assert_contents> 191 label="QC: Min number of tiles missing for Ambiguous Result"
192 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/> 192 help="default = 3"/>
193 </assert_contents> 193 <param name="max_missing_tiles" type="float"
194 </output> 194 argument="--max-missing-tiles"
195 </test> 195 optional="true"
196 <test> 196 value="0.05" min="0" max="1"
197 <param name="type" value="paired"/> 197 label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/>
198 <param name="type_of_scheme" value="heidelberg"/> 198 <param name="max_intermediate_tiles" type="float"
199 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/> 199 argument="--max-intermediate-tiles"
200 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/> 200 optional="true"
201 <output name="results.tab"> 201 value="0.05" min="0" max="1"
202 <assert_contents> 202 label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype"
203 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+avg_tile_coverage\s+qc_status\s+qc_message"/> 203 help="default = 0.05, valid values {0.0 - 1.0}"/>
204 </assert_contents> 204 <param name="low_coverage_warning" type="integer"
205 </output> 205 argument="--low-cov-warning"
206 <output name="match_results.tab"> 206 optional="true"
207 <assert_contents> 207 value="20"
208 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> 208 label="QC: Overall tile coverage below this value will trigger a low coverage warning"
209 </assert_contents> 209 help="default = 20"/>
210 </output> 210 </section>
211 <output name="tech_results.tab"> 211 <section name="dev_args" title="Developer Options" expanded="False">
212 <assert_contents> 212 <param name="use_json"
213 <has_text_matching expression="sample\s+subtype\s+avg_tile_coverage\s+qc_status\s+qc_message"/> 213 type="boolean"
214 </assert_contents> 214 checked="false"
215 </output> 215 truevalue="--json"
216 </test> 216 falsevalue=""
217 </tests> 217 label="Output JSON results"
218 <help><![CDATA[ 218 help="Use this option of you need json representations of analysis' details"/>
219 </section>
220 </inputs>
221 <outputs>
222 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
223 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
224 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
225 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
226 <filter>dev_args['use_json']</filter>
227 </data>
228 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
229 <filter>dev_args['use_json']</filter>
230 </data>
231 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
232 <filter>dev_args['use_json']</filter>
233 </data>
234 </outputs>
235 <tests>
236 <test>
237 <conditional name="input">
238 <param name="type" value="fasta"/>
239 <param name="fasta" value="SRR1002850_SMALL.fasta"/>
240 </conditional>
241 <param name="type_of_scheme" value="heidelberg"/>
242 <output name="results.tab"
243 value="SRR1002850_SMALL.fasta-results.tab"
244 ftype="tabular"
245 compare="sim_size"
246 delta="1000">
247 </output>
248 <output name="match_results.tab"
249 value="SRR1002850_SMALL.fasta-match_results.tab"
250 ftype="tabular"
251 compare="sim_size"
252 delta="16000">
253 </output>
254 <output name="tech_results.tab"
255 value="SRR1002850_SMALL.fasta-tech_results.tab"
256 ftype="tabular"
257 lines_diff="0">
258 </output>
259 </test>
260 <test>
261 <conditional name="input">
262 <param name="type" value="paired"/>
263 <param name="forward" value="SRR5646583_SMALL_1.fastq"/>
264 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/>
265 </conditional>
266 <param name="type_of_scheme" value="heidelberg"/>
267 <output name="tech_results.tab"
268 value="SRR5646583_SMALL-tech_results.tab"
269 ftype="tabular"
270 lines_diff="0">
271 </output>
272 <output name="results.tab"
273 value="SRR5646583_SMALL-results.tab"
274 ftype="tabular"
275 compare="sim_size"
276 delta="1000">
277 </output>
278 <output name="match_results.tab"
279 value="SRR5646583_SMALL-match_results.tab"
280 ftype="tabular"
281 compare="sim_size"
282 delta="16000">
283 </output>
284 </test>
285 </tests>
286 <help><![CDATA[
219 *********************************************************** 287 ***********************************************************
220 bio_hansel - Heidelberg And eNteritidis Snp ELucidation 288 bio_hansel
221 *********************************************************** 289 ***********************************************************
222 290
223 Subtype *Salmonella enterica* subsp. enterica serovar Heidelberg and Enteritidis genomes using *in-silico* 33 bp k-mer SNP subtyping schemes developed by Genevieve Labbe et al. 291 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide variant (SNV) targeting k-mer subtyping schemes.
224 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)! 292
293 Includes 33 bp k-mer SNV subtyping schemes for Salmonella enterica subsp. enterica serovar Heidelberg and Enteritidis genomes developed by Genevieve Labbe et al.
225 294
226 Usage 295 Usage
227 ===== 296 =====
228 1) Enter your FASTA/FASTQ file(s) 297 1) Enter your FASTA/FASTQ file(s)
229 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own) 298 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own)
239 ------------------------------- 308 -------------------------------
240 309
241 310
242 Contents of ``results.tab``: 311 Contents of ``results.tab``:
243 312
244 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+ 313 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
245 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path | 314 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | qc_status | qc_message |
246 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+ 315 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
247 | file.fasta | heidelberg | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 1037658-2.2.2.2.1.4; 2154958-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | file.fasta | 316 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | |
248 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+ 317 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
249
250 318
251 319
252 Contents of ``match_results.tab``: 320 Contents of ``match_results.tab``:
253 321
254 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ 322 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
255 | tilename | stitle | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | qlen | slen | seq | coverage | is_trunc | refposition | subtype | is_pos_tile | sample | file_path | scheme | 323 | tilename | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_tile | sample | file_path | scheme | scheme_version | qc_status | qc_message |
256 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ 324 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
257 | 775920-2.2.2.2 | NODE_2_length_512016_cov_46.4737_ID_3 | 100 | 33 | 0 | 0 | 1 | 33 | 474875 | 474907 | 2E-11 | 62.1 | 33 | 512016 | GTTCAGGTGCTACCGAGGATCGTTTTTGGTGCG | 1 | False | 775920 | 2.2.2.2 | True | out | file.fasta | heidelberg | 325 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
258 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ 326 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
259 | negative3305400-2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 276235 | 276267 | 2E-11 | 62.1 | 33 | 427905 | CATCGTGAAGCAGAACAGACGCGCATTCTTGCT | 1 | False | negative3305400 | 2.1.1.1 | False | out | file.fasta | heidelberg | 327 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
260 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ 328 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
261 | negative3200083-2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 170918 | 170950 | 2E-11 | 62.1 | 33 | 427905 | ACCCGGTCTACCGCAAAATGGAAAGCGATATGC | 1 | False | negative3200083 | 2.1 | False | out | file.fasta | heidelberg | 329
262 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+ 330 *Next 201 lines omitted.*
263 | negative3204925-2.2.3.1.5 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 175760 | 175792 | 2E-11 | 62.1 | 33 | 427905 | CTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG | 1 | False | negative3204925 | 2.2.3.1.5 | False | out | file.fasta | heidelberg |
264 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
265 | negative3230678-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 201513 | 201545 | 2E-11 | 62.1 | 33 | 427905 | AGCGGTGCGCCAAACCACCCGGAATGATGAGTG | 1 | False | negative3230678 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg |
266 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
267 | negative3233869-2.1.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 204704 | 204736 | 2E-11 | 62.1 | 33 | 427905 | CAGCGCTGGTATGTGGCTGCACCATCGTCATTA | 1 | False | negative3233869 | 2.1.1.1.1 | False | out | file.fasta | heidelberg |
268 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
269 | negative3254229-2.2.3.1.3 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 225064 | 225096 | 2E-11 | 62.1 | 33 | 427905 | CGCCACCACGCGGTTAGCGTCACGCTGACATTC | 1 | False | negative3254229 | 2.2.3.1.3 | False | out | file.fasta | heidelberg |
270 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
271 | negative3257074-2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 227909 | 227941 | 2E-11 | 62.1 | 33 | 427905 | CGGCAACCAGACCGACTACGCCGCCAAGCAGAC | 1 | False | negative3257074 | 2.2.1 | False | out | file.fasta | heidelberg |
272 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
273 | negative3264474-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 235309 | 235341 | 2E-11 | 62.1 | 33 | 427905 | AATGGCGCCGATCGTCGCCAGATAACCGTTGCC | 1 | False | negative3264474 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg |
274 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
275 | negative3267927-2.2.2.2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 238762 | 238794 | 2E-11 | 62.1 | 33 | 427905 | AAAGAGAAATATGATGCCAGGCTGATACATGAC | 1 | False | negative3267927 | 2.2.2.2.2.1 | False | out | file.fasta | heidelberg |
276 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
277 | negative3278067-1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 248902 | 248934 | 2E-11 | 62.1 | 33 | 427905 | TGTGAGTAAGTTGCGCGATATTCTGCTGGATTC | 1 | False | negative3278067 | 1.1 | False | out | file.fasta | heidelberg |
278 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
279 | negative3299717-2.2.3.1.4 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 270552 | 270584 | 2E-11 | 62.1 | 33 | 427905 | ATGCCGGACAGCAGGCGAAACTCGAACCGGATA | 1 | False | negative3299717 | 2.2.3.1.4 | False | out | file.fasta | heidelberg |
280 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
281 | negative3373069-2.2.2.2.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 344011 | 344043 | 2E-11 | 62.1 | 33 | 427905 | CTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA | 1 | False | negative3373069 | 2.2.2.2.1.1 | False | out | file.fasta | heidelberg |
282 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
283
284 Next 196 lines omitted.
285 331
286 332
287 333
288 Analysis of a single FASTQ readset 334 Analysis of a single FASTQ readset
289 ---------------------------------- 335 ----------------------------------
290 336
291 Contents of ``results.tab``: 337 Contents of ``results.tab``:
292 338
293 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+ 339 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
294 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path | 340 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | avg_tile_coverage | qc_status | qc_message |
295 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+ 341 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
296 | 564 | heidelberg | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | forward.fastqsanger; reverse.fastqsanger | 342 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | |
297 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+ 343 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
298
299 344
300 Contents of ``match_results.tab``: 345 Contents of ``match_results.tab``:
301 346
302 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ 347 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
303 | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme | 348 | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |
304 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ 349 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
305 | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg | 350 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
306 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ 351 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
307 | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg | 352 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
308 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ 353 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
309 | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg | 354
310 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ 355 *Next 202 lines omitted.*
311 | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg | 356
312 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+ 357 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.
313 | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |
314 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
315 | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |
316 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
317
318 Next 200 lines omitted.
319
320 Galaxy wrapper written by Matthew Gopez at the Public Health Agency of Canada, National Microbiology Laboratory.
321 358
322 ]]></help> 359 ]]></help>
323 <citations> 360 <citations>
324 <citation type="bibtex">@ARTICLE{a1, 361 <citation type="bibtex">@ARTICLE{a1,
325 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.}, 362 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},
326 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash.}, 363 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},
327 url = {https://github.com/phac-nml/bio_hansel} 364 url = {https://github.com/phac-nml/bio_hansel}
328 } 365 }
329 }</citation> 366 }</citation>
330 </citations> 367 </citations>
331 </tool> 368 </tool>