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comparison mlst.xml @ 3:68cdb40ff91c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 829727d4bc801d4422680e018c2873bbab2e6a67
author iuc
date Mon, 15 Oct 2018 07:41:48 -0400
parents 253b7a1cf87e
children 1f5641a52664
comparison
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2:253b7a1cf87e 3:68cdb40ff91c
1 <tool id="mlst" name="MLST" version="2.10"> 1 <tool id="mlst" name="MLST" version="@VERSION@">
2 <requirements> 2 <description>Scans genomes against PubMLST schemes.</description>
3 <requirement type="package" version="2.10">mlst</requirement> 3 <macros>
4 </requirements> 4 <import>macros.xml</import>
5 5
6 <version_command>mlst --version</version_command> 6 <xml name="legacy_param">
7 7 <param argument="--legacy" type="boolean" truevalue="--legacy" falsevalue="" checked="true" label="Include allele header" help="Include allele header row in output table (requires scheme to be set)" />
8 <command detect_errors="exit_code"><![CDATA[ 8 </xml>
9 mlst "$input_file" --nopath 9 </macros>
10 #if $settings.advanced == "advanced" 10 <expand macro="requirements" />
11 #if $settings.min_dna_id 11 <expand macro="version_command" />
12 --minid=$settings.min_dna_id 12
13 <command detect_errors="aggressive"><![CDATA[
14 #import re
15
16 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
17 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
18 #set $named_input_files = ''
19 #for $input_file in $input_files
20 ## Add single quotes around each input file identifier
21 #set $_input_file = "'{}'".format($input_file.element_identifier)
22 ln -s '${input_file}' ${_input_file} &&
23 #set $named_input_files = $named_input_files + ' ' + $_input_file
24 #end for
25
26 mlst --nopath
27 --threads "\${GALAXY_SLOTS:-1}"
28 #if str($settings.advanced) == "advanced"
29 #if str($settings.minid)
30 --minid=$settings.minid
13 #end if 31 #end if
14 #if $settings.min_dna_cov 32 #if str($settings.mincov)
15 --mincov=$settings.min_dna_cov 33 --mincov=$settings.mincov
16 #end if 34 #end if
17 #if $settings.scheme 35 #if $settings.novel
18 --scheme=$settings.scheme 36 --novel '${novel_alleles}'
37 #end if
38 #if str($settings.scheme_condition.set_scheme) == "auto"
39 #if str($settings.scheme_condition.minscore)
40 --minscore=$settings.scheme_condition.minscore
41 #end if
42 #if str($settings.scheme_condition.exclude)
43 --exclude '${settings.scheme_condition.exclude}'
44 #end if
45 #elif str($settings.scheme_condition.set_scheme) == "list" or str($settings.scheme_condition.set_scheme) == "manual"
46 #if str($settings.scheme_condition.scheme)
47 --scheme='${settings.scheme_condition.scheme}'
48 #end if
49 $settings.scheme_condition.legacy
19 #end if 50 #end if
20 #end if 51 #end if
52 ${named_input_files}
21 > "$report" 53 > "$report"
22 ]]></command> 54 ]]></command>
23 55
24 <inputs> 56 <inputs>
25 <param type="data" name="input_file" format="fasta,genbank" /> 57 <param type="data" name="input_files" format="fasta,genbank" multiple="true" />
26 <conditional name="settings"> 58 <conditional name="settings">
27 <param name="advanced" type="select" label="Specify advanced parameters"> 59 <param name="advanced" type="select" label="Specify advanced parameters">
28 <option value="simple" selected="true">No, use program defaults.</option> 60 <option value="simple" selected="true">No, use program defaults.</option>
29 <option value="advanced">Yes, see full parameter list.</option> 61 <option value="advanced">Yes, see full parameter list.</option>
30 </param> 62 </param>
31 <when value="simple"> 63 <when value="simple">
32 </when> 64 </when>
33 <when value="advanced"> 65 <when value="advanced">
34 <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" /> 66 <param argument="--minid" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
35 <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" /> 67 <param argument="--mincov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
36 <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" /> 68 <param argument="--novel" type="boolean" checked="false" label="Output novel alleles" />
69 <conditional name="scheme_condition">
70 <param name="set_scheme" type="select" label="Automatically set MLST scheme">
71 <option value="auto" selected="true">Automatic MLST scheme detection</option>
72 <option value="list">Select from a list of MLST schemes</option>
73 <option value="manual">Manually set MLST scheme</option>
74 </param>
75 <when value="auto">
76 <param argument="--minscore" type="integer" label="Minimum score to match scheme" value="50" min="0" max="100" help="Minumum score out of 100 to match a scheme" optional="true" />
77 <param argument="--exclude" type="text" area="false" label="Exclude these schemes" help="Ignore these schemes from auto detection (comma sep. list) (default 'ecoli_2,abaumannii')" optional="true" />
78 </when>
79 <when value="list">
80 <param argument="--scheme" type="select" label="PubMLST Scheme (list)" help="Select a MLST scheme">
81 <option value="achromobacter">achromobacter</option>
82 <option value="vvulnificus">vvulnificus</option>
83 <option value="cglabrata">cglabrata</option>
84 <option value="sthermophilus_2">sthermophilus_2</option>
85 <option value="mmassiliense">mmassiliense</option>
86 <option value="bhampsonii">bhampsonii</option>
87 <option value="afumigatus">afumigatus</option>
88 <option value="ecloacae">ecloacae</option>
89 <option value="brucella">brucella</option>
90 <option value="spseudintermedius">spseudintermedius</option>
91 <option value="kpneumoniae">kpneumoniae</option>
92 <option value="edwardsiella">edwardsiella</option>
93 <option value="chlamydiales">chlamydiales</option>
94 <option value="leptospira_2">leptospira_2</option>
95 <option value="neisseria">neisseria</option>
96 <option value="vcholerae">vcholerae</option>
97 <option value="orhinotracheale">orhinotracheale</option>
98 <option value="paeruginosa">paeruginosa</option>
99 <option value="lsalivarius">lsalivarius</option>
100 <option value="leptospira">leptospira</option>
101 <option value="sepidermidis">sepidermidis</option>
102 <option value="mhyorhinis">mhyorhinis</option>
103 <option value="bcc">bcc</option>
104 <option value="yruckeri">yruckeri</option>
105 <option value="suberis">suberis</option>
106 <option value="yersinia">yersinia</option>
107 <option value="taylorella">taylorella</option>
108 <option value="kaerogenes">kaerogenes</option>
109 <option value="xfastidiosa">xfastidiosa</option>
110 <option value="bordetella">bordetella</option>
111 <option value="cbotulinum">cbotulinum</option>
112 <option value="hpylori">hpylori</option>
113 <option value="mpneumoniae">mpneumoniae</option>
114 <option value="sdysgalactiae">sdysgalactiae</option>
115 <option value="efaecium">efaecium</option>
116 <option value="aphagocytophilum">aphagocytophilum</option>
117 <option value="ecoli_2">ecoli_2</option>
118 <option value="ganatis">ganatis</option>
119 <option value="mhyopneumoniae">mhyopneumoniae</option>
120 <option value="bsubtilis">bsubtilis</option>
121 <option value="tenacibaculum">tenacibaculum</option>
122 <option value="campylobacter">campylobacter</option>
123 <option value="ranatipestifer">ranatipestifer</option>
124 <option value="mcaseolyticus">mcaseolyticus</option>
125 <option value="csputorum">csputorum</option>
126 <option value="csinensis">csinensis</option>
127 <option value="dnodosus">dnodosus</option>
128 <option value="koxytoca">koxytoca</option>
129 <option value="soralis">soralis</option>
130 <option value="bcereus">bcereus</option>
131 <option value="wolbachia">wolbachia</option>
132 <option value="saureus">saureus</option>
133 <option value="hcinaedi">hcinaedi</option>
134 <option value="clari">clari</option>
135 <option value="leptospira_3">leptospira_3</option>
136 <option value="sinorhizobium">sinorhizobium</option>
137 <option value="pmultocida_multihost">pmultocida_multihost</option>
138 <option value="ecoli">ecoli</option>
139 <option value="pdamselae">pdamselae</option>
140 <option value="pmultocida_rirdc">pmultocida_rirdc</option>
141 <option value="bhyodysenteriae">bhyodysenteriae</option>
142 <option value="cupsaliensis">cupsaliensis</option>
143 <option value="efaecalis">efaecalis</option>
144 <option value="shaemolyticus">shaemolyticus</option>
145 <option value="rhodococcus">rhodococcus</option>
146 <option value="pacnes">pacnes</option>
147 <option value="szooepidemicus">szooepidemicus</option>
148 <option value="pgingivalis">pgingivalis</option>
149 <option value="cfetus">cfetus</option>
150 <option value="bpilosicoli">bpilosicoli</option>
151 <option value="kseptempunctata">kseptempunctata</option>
152 <option value="streptomyces">streptomyces</option>
153 <option value="smaltophilia">smaltophilia</option>
154 <option value="ppentosaceus">ppentosaceus</option>
155 <option value="cronobacter">cronobacter</option>
156 <option value="mhaemolytica">mhaemolytica</option>
157 <option value="cdiphtheriae">cdiphtheriae</option>
158 <option value="vcholerae2">vcholerae2</option>
159 <option value="chyointestinalis">chyointestinalis</option>
160 <option value="borrelia">borrelia</option>
161 <option value="abaumannii">abaumannii</option>
162 <option value="arcobacter">arcobacter</option>
163 <option value="csepticum">csepticum</option>
164 <option value="mcanis">mcanis</option>
165 <option value="pfluorescens">pfluorescens</option>
166 <option value="lmonocytogenes">lmonocytogenes</option>
167 <option value="sgallolyticus">sgallolyticus</option>
168 <option value="cfreundii">cfreundii</option>
169 <option value="mplutonius">mplutonius</option>
170 <option value="vibrio">vibrio</option>
171 <option value="bbacilliformis">bbacilliformis</option>
172 <option value="ypseudotuberculosis">ypseudotuberculosis</option>
173 <option value="vparahaemolyticus">vparahaemolyticus</option>
174 <option value="mcatarrhalis">mcatarrhalis</option>
175 <option value="bintermedia">bintermedia</option>
176 <option value="sagalactiae">sagalactiae</option>
177 <option value="kkingae">kkingae</option>
178 <option value="bpseudomallei">bpseudomallei</option>
179 <option value="bhenselae">bhenselae</option>
180 <option value="spneumoniae">spneumoniae</option>
181 <option value="vtapetis">vtapetis</option>
182 <option value="senterica">senterica</option>
183 <option value="mabscessus">mabscessus</option>
184 <option value="sthermophilus">sthermophilus</option>
185 <option value="brachyspira">brachyspira</option>
186 <option value="mbovis">mbovis</option>
187 <option value="hsuis">hsuis</option>
188 <option value="spyogenes">spyogenes</option>
189 <option value="cconcisus">cconcisus</option>
190 <option value="cmaltaromaticum">cmaltaromaticum</option>
191 <option value="abaumannii_2">abaumannii_2</option>
192 <option value="aeromonas">aeromonas</option>
193 <option value="miowae">miowae</option>
194 <option value="shominis">shominis</option>
195 <option value="otsutsugamushi">otsutsugamushi</option>
196 <option value="hinfluenzae">hinfluenzae</option>
197 <option value="clanienae">clanienae</option>
198 <option value="sbsec">sbsec</option>
199 <option value="scanis">scanis</option>
200 <option value="msynoviae">msynoviae</option>
201 <option value="hparasuis">hparasuis</option>
202 <option value="magalactiae">magalactiae</option>
203 <option value="chelveticus">chelveticus</option>
204 <option value="fpsychrophilum">fpsychrophilum</option>
205 <option value="ssuis">ssuis</option>
206 <option value="cdifficile">cdifficile</option>
207 <option value="cinsulaenigrae">cinsulaenigrae</option>
208 <option value="blicheniformis">blicheniformis</option>
209 <option value="slugdunensis">slugdunensis</option>
210 <option value="plarvae">plarvae</option>
211 </param>
212 <expand macro="legacy_param" />
213 </when>
214 <when value="manual">
215 <param name="scheme" type="text" area="false" label="MLST Scheme (manual)" help="Enter a MLST scheme to use (see output of 'MLST List' tool for a list of available schemes)" />
216 <expand macro="legacy_param" />
217 </when>
218 </conditional>
37 </when> 219 </when>
38 </conditional> 220 </conditional>
39 </inputs> 221 </inputs>
40 222
41 <outputs> 223 <outputs>
42 <data name="report" format="tabular" /> 224 <data name="report" format="tabular" label="${tool.name} on ${on_string}: report.tsv"/>
225 <data name="novel_alleles" format="fasta" label="${tool.name} on ${on_string}: novel_alleles.fasta">
226 <filter>settings['advanced'] == "advanced" and settings['novel']</filter>
227 </data>
43 </outputs> 228 </outputs>
44 229
45 <tests> 230 <tests>
46 <!-- Basic test - will produce no results. --> 231 <!-- Basic test - will produce no results. -->
47 <test> 232 <test>
48 <param name="input_file" value="Acetobacter.fna"/> 233 <param name="input_files" value="Acetobacter.fna"/>
49 <param name="advanced" value="simple"/> 234 <param name="advanced" value="simple"/>
50 <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/> 235 <output name="report" ftype="tabular" file="output_noresults.txt"/>
51 </test> 236 </test>
52 237
53 <!-- Basic test - will produce results. --> 238 <!-- Basic test - will produce results. -->
54 <test> 239 <test>
55 <param name="input_file" value="MRSA0252_trimmed.fna"/> 240 <param name="input_files" value="MRSA0252_trimmed.fna"/>
56 <param name="advanced" value="simple"/> 241 <param name="advanced" value="simple"/>
57 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/> 242 <output name="report" ftype="tabular" file="output_mrsa.txt"/>
58 </test> 243 </test>
59 244
60 <!-- Advanced test - Min DNA Coverage 100 --> 245 <!-- Advanced test - Min DNA Coverage 100 -->
61 <test> 246 <test>
62 <param name="input_file" value="MRSA0252_trimmed.fna"/> 247 <param name="input_files" value="MRSA0252_trimmed.fna"/>
63 <param name="advanced" value="advanced"/> 248 <param name="advanced" value="advanced"/>
64 <param name="min_dna_cov" value="100"/> 249 <param name="mincov" value="100"/>
65 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/> 250 <output name="report" ftype="tabular" file="output_mincov100.txt"/>
66 </test> 251 </test>
67 252
68 <!-- Advanced test - Min DNA ID 100 --> 253 <!-- Advanced test - Min DNA ID 100 -->
69 <test> 254 <test>
70 <param name="input_file" value="MRSA0252_trimmed.fna"/> 255 <param name="input_files" value="MRSA0252_trimmed.fna"/>
71 <param name="advanced" value="advanced"/> 256 <param name="advanced" value="advanced"/>
72 <param name="min_dna_id" value="100"/> 257 <param name="minid" value="100"/>
73 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/> 258 <output name="report" ftype="tabular" file="output_minid100.txt"/>
259 </test>
260
261 <!-- Advanced test - Manually set MLST scheme -->
262 <test>
263 <param name="input_files" value="MRSA0252_trimmed.fna"/>
264 <param name="advanced" value="advanced"/>
265 <param name="set_scheme" value="manual"/>
266 <param name="scheme" value="saureus"/>
267 <param name="legacy" value="true"/>
268 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
269 </test>
270
271 <!-- Advanced test - Set a MLST scheme from a list -->
272 <test>
273 <param name="input_files" value="MRSA0252_trimmed.fna"/>
274 <param name="advanced" value="advanced"/>
275 <param name="set_scheme" value="list"/>
276 <param name="scheme" value="saureus"/>
277 <param name="legacy" value="true"/>
278 <output name="report" ftype="tabular" file="output_mrsa_legacy.txt"/>
279 </test>
280
281 <!-- Advanced test - exclude scheme -->
282 <test>
283 <param name="input_files" value="MRSA0252_trimmed.fna"/>
284 <param name="advanced" value="advanced"/>
285 <param name="set_scheme" value="auto"/>
286 <param name="exclude" value="saureus"/>
287 <param name="legacy" value="false"/>
288 <output name="report" ftype="tabular" file="output_mrsa_exclude.txt"/>
289 </test>
290
291 <!-- Advanced test - output novel alleles. -->
292 <test>
293 <param name="input_files" value="MRSA0252_trimmed_novel.fna"/>
294 <param name="advanced" value="advanced"/>
295 <param name="minid" value="98"/>
296 <param name="novel" value="true"/>
297 <param name="set_scheme" value="manual"/>
298 <param name="scheme" value="saureus"/>
299 <param name="legacy" value="false"/>
300 <output name="report" ftype="tabular" file="output_mrsa_novel.txt"/>
301 <output name="novel_alleles" ftype="fasta" file="output_mrsa_novel.fasta"/>
74 </test> 302 </test>
75 </tests> 303 </tests>
76 304
77 <help><![CDATA[ 305 <help><![CDATA[
78 **What it does** 306 **What it does**
93 321
94 genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3) 322 genomes/6008.fna saureus 239 arcc(2) aroe(3) glpf(1) gmk_(1) pta_(4) tpi_(4) yqil(3)
95 323
96 **Without auto-detection** 324 **Without auto-detection**
97 325
98 If you provide the 'scheme' parameter, it will print a fixed tabular output with a heading containing allele names specific to that scheme. To view a list of schemes, use the MLST List tool. 326 If you choose to manually set the MLST scheme, it will print a fixed tabular output with a heading containing allele names specific to that scheme (adjustable with **Include allele header**). To view a list of schemes, use the MLST List tool.
99 327
100 :: 328 ::
101 329
102 FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm 330 FILE SCHEME ST abcZ adk aroE fumC gdh pdhC pgm
103 NM003.fa neisseria 11 2 3 4 3 8 4 6 331 NM003.fa neisseria 11 2 3 4 3 8 4 6
104 332
105 **Missing data** 333 **Missing data**
334
106 MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below: 335 MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below:
107 336
108 +--------+---------------------------+ 337 +--------+---------------------------------------+
109 | Symbol | Meaning | 338 | Symbol | Meaning |
110 +========+===========================+ 339 +========+=======================================+
111 | n | Exact intact allele | 340 | n | Exact intact allele |
112 +--------+---------------------------+ 341 +--------+---------------------------------------+
113 | ~n | Novel allele similar to n | 342 | ~n | Novel full length allele similar to n |
114 +--------+---------------------------+ 343 +--------+---------------------------------------+
115 | n,m | Multiple alleles | 344 | n? | Partial match to known allele |
116 +--------+---------------------------+ 345 +--------+---------------------------------------+
117 | *-* | Allele missing | 346 | n,m | Multiple alleles |
118 +--------+---------------------------+ 347 +--------+---------------------------------------+
348 | *-* | Allele missing |
349 +--------+---------------------------------------+
350
351 Setting **Output novel alleles** to true will produce an additional **novel_alleles.fasta** file containing the novel alleles.
119 352
120 Galaxy wrapper maintained by Simon Gladman. 353 Galaxy wrapper maintained by Simon Gladman.
121 ]]></help> 354 ]]></help>
122 355
123 <citations> 356 <expand macro="citations" />
124 <citation type="bibtex">
125 @UNPUBLISHED{Seemann2016,
126 author = "Seemann T",
127 title = "MLST: Scan contig files against PubMLST typing schemes",
128 year = "2016",
129 note = "https://github.com/tseemann/mlst"}
130 </citation>
131 </citations>
132 </tool> 357 </tool>