Mercurial > repos > iuc > spades_plasmidspades
comparison plasmidspades.xml @ 0:eabeb1a74dac draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author | iuc |
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date | Sun, 23 Jan 2022 21:32:59 +0000 |
parents | |
children | 6aad515a5270 |
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1 <tool id="spades_plasmidspades" name="plasmidSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> | |
2 <description>extract and assembly plasmids from WGS data</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 | |
11 #set $library = 1 | |
12 | |
13 @PREPROCESS_INPUT_FILES_MAIN@ | |
14 #if $additional_reads.selector == 'true' | |
15 @PREPROCESS_INPUT_FILES_ADDITIONAL@ | |
16 #end if | |
17 @PREPROCESS_NANOPORE_PACBIO_FILES@ | |
18 @PREPROCESS_SANGER_FILES@ | |
19 @PREPROCESS_CONTIGS_FILES@ | |
20 @PREPROCESS_ASSEMBLY_GRAPH_FILES@ | |
21 | |
22 ## run | |
23 plasmidspades.py | |
24 $operation_mode | |
25 -o 'output' | |
26 @RESOURCES@ | |
27 @INPUT_READS_MAIN@ | |
28 #if $additional_reads.selector == 'true' | |
29 @INPUT_READS_ADDITIONAL@ | |
30 #end if | |
31 ## reads | |
32 @NANOPORE_PACBIO@ | |
33 @SANGER@ | |
34 @CONTIGS@ | |
35 @ASSEMBLY_GRAPH@ | |
36 ## parameter | |
37 --cov-cutoff $cov_cond.cov_cutoff | |
38 @KMER@ | |
39 @PIPELINE_OPTIONS@ | |
40 @PHREDOFFSET@ | |
41 ## postprocessing | |
42 @STATS@ | |
43 @CORRECTED@ | |
44 ]]></command> | |
45 <inputs> | |
46 <expand macro="operation_mode"/> | |
47 <expand macro="input_files_all" format="fastq, fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/> | |
48 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/> | |
49 <section name="arf" title="Additional read files"> | |
50 <expand macro="nanopore_pacbio"/> | |
51 <expand macro="sanger"/> | |
52 <expand macro="contigs"/> | |
53 <expand macro="assembly_graph"/> | |
54 </section> | |
55 <expand macro="pipeline_options"> | |
56 <option value="--careful">Careful: tries to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option> | |
57 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> | |
58 </expand> | |
59 <expand macro="covcutoff"/> | |
60 <expand macro="kmer"/> | |
61 <expand macro="phred"/> | |
62 <expand macro="optional_output"/> | |
63 </inputs> | |
64 <outputs> | |
65 <expand macro="out_ag"/> | |
66 <expand macro="out_ags"/> | |
67 <expand macro="out_cn"/> | |
68 <expand macro="out_cp"/> | |
69 <expand macro="out_cr"/> | |
70 <expand macro="out_cs"/> | |
71 <expand macro="out_l"/> | |
72 <expand macro="out_sc"/> | |
73 <expand macro="out_sp"/> | |
74 <expand macro="out_ss"/> | |
75 </outputs> | |
76 <tests> | |
77 <!-- | |
78 used in a test: | |
79 single library: 12, 1, 2 | |
80 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or> | |
81 k, phred-offset, disablerr, iontorrent, careful, only-assembler, only-error-correction | |
82 | |
83 not used in a test: | |
84 single library: merged, s | |
85 multiple libraries: pe#-m, pe#-s, mp#-12, mp#-1, mp#-2, mp#-<or>, mp#-s, hqmp#-12, hqmp#-1, hqmp#-2, hqmp#-s, hqmp#-<or>, nxmate#-1, nxmate-#2 | |
86 pacbio, nanopore, sanger, trusted-contigs, untrusted-contigs, tslr | |
87 --> | |
88 | |
89 <!-- #1 single, separate, fastq.gz, default parameters --> | |
90 <test expect_num_outputs="4"> | |
91 <conditional name="singlePaired"> | |
92 <param name="sPaired" value="paired"/> | |
93 <param name="input1" value="pl1.fq.gz"/> | |
94 <param name="input2" value="pl2.fq.gz"/> | |
95 </conditional> | |
96 <output name="out_ag"> | |
97 <assert_contents> | |
98 <has_n_lines n="326"/> | |
99 <has_text_matching expression=">EDGE_22_length_9689_cov_4.668331:EDGE_22_length_9689_cov_4.668331"/> | |
100 </assert_contents> | |
101 </output> | |
102 <output name="out_ags"> | |
103 <assert_contents> | |
104 <has_n_lines n="3"/> | |
105 <has_text_matching expression="S.+"/> | |
106 </assert_contents> | |
107 </output> | |
108 <output name="out_cn"> | |
109 <assert_contents> | |
110 <has_n_lines n="163"/> | |
111 <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/> | |
112 </assert_contents> | |
113 </output> | |
114 <output name="out_sc"> | |
115 <assert_contents> | |
116 <has_n_lines n="163"/> | |
117 <has_text_matching expression=">NODE\_1\_length\_9689.+"/> | |
118 </assert_contents> | |
119 </output> | |
120 </test> | |
121 <!-- #2 single, separate, fastq, all outputs and custom parameters --> | |
122 <test expect_num_outputs="10"> | |
123 <conditional name="singlePaired"> | |
124 <param name="sPaired" value="paired"/> | |
125 <param name="input1" value="pl1.fq.gz"/> | |
126 <param name="input2" value="pl2.fq.gz"/> | |
127 </conditional> | |
128 <conditional name="cov_cond"> | |
129 <param name="cov_sel" value="auto"/> | |
130 </conditional> | |
131 <param name="phred_offset" value="33"/> | |
132 <param name="optional_output" value="ag,ags,cn,cp,cr,cs,l,sc,sp,ss"/> | |
133 <output name="out_ag"> | |
134 <assert_contents> | |
135 <has_n_lines n="326"/> | |
136 <has_text_matching expression=">EDGE_.+"/> | |
137 </assert_contents> | |
138 </output> | |
139 <output name="out_ags"> | |
140 <assert_contents> | |
141 <has_n_lines n="3"/> | |
142 <has_text_matching expression="S.+"/> | |
143 </assert_contents> | |
144 </output> | |
145 <output name="out_cn"> | |
146 <assert_contents> | |
147 <has_n_lines n="163"/> | |
148 <has_text_matching expression=">NODE.+"/> | |
149 </assert_contents> | |
150 </output> | |
151 <output name="out_cp"> | |
152 <assert_contents> | |
153 <has_n_lines n="4"/> | |
154 </assert_contents> | |
155 </output> | |
156 <output name="out_cs"> | |
157 <assert_contents> | |
158 <has_n_lines n="1"/> | |
159 <has_text_matching expression="#name	length	coverage"/> | |
160 </assert_contents> | |
161 </output> | |
162 <output_collection name="out_cr" type="list" count="3"> | |
163 <element name="pl1.fq.gz.fastq.00.0_0.cor"> | |
164 <assert_contents> | |
165 <has_size value="72173" delta="1000"/> | |
166 </assert_contents> | |
167 </element> | |
168 <element name="pl2.fq.gz.fastq.00.0_0.cor"> | |
169 <assert_contents> | |
170 <has_size value="72173" delta="1000"/> | |
171 </assert_contents> | |
172 </element> | |
173 <element name="pl_unpaired.00.0_0.cor"> | |
174 <assert_contents> | |
175 <has_size value="392" delta="100"/> | |
176 </assert_contents> | |
177 </element> | |
178 </output_collection> | |
179 <output name="out_l"> | |
180 <assert_contents> | |
181 <has_text_matching expression="Thank you for using SPAdes!"/> | |
182 </assert_contents> | |
183 </output> | |
184 <output name="out_sc"> | |
185 <assert_contents> | |
186 <has_n_lines n="163"/> | |
187 </assert_contents> | |
188 </output> | |
189 <output name="out_sp"> | |
190 <assert_contents> | |
191 <has_n_lines n="4"/> | |
192 </assert_contents> | |
193 </output> | |
194 <output name="out_ss"> | |
195 <assert_contents> | |
196 <has_n_lines n="1"/> | |
197 </assert_contents> | |
198 </output> | |
199 </test> | |
200 <!-- #3 multiple, single & paired-end, test dataset not valid --> | |
201 <test expect_num_outputs="1"> | |
202 <param name="operation_mode" value="--only-assembler"/> | |
203 <conditional name="singlePaired"> | |
204 <param name="sPaired" value="interlaced"/> | |
205 <param name="input1" value="ecoli_1K.fastq.gz"/> | |
206 </conditional> | |
207 <conditional name="additional_reads"> | |
208 <param name="selector" value="true"/> | |
209 <conditional name="singlePaired"> | |
210 <param name="sPaired" value="paired"/> | |
211 <param name="input1" value="pl1.fq.gz"/> | |
212 <param name="input2" value="pl2.fq.gz"/> | |
213 </conditional> | |
214 <param name="type_paired" value="mp"/> | |
215 <param name="orientation" value="rf"/> | |
216 </conditional> | |
217 <param name="mode_sel" value="--careful"/> | |
218 <param name="optional_output" value="l"/> | |
219 <output name="out_l"> | |
220 <assert_contents> | |
221 <has_text_matching expression="Thank you for using SPAdes!"/> | |
222 </assert_contents> | |
223 </output> | |
224 </test> | |
225 <!-- #4 test dataset not valid--> | |
226 <test expect_num_outputs="1"> | |
227 <conditional name="singlePaired"> | |
228 <param name="sPaired" value="paired"/> | |
229 <param name="input1" value="pl1.fq.gz"/> | |
230 <param name="input2" value="pl2.fq.gz"/> | |
231 </conditional> | |
232 <param name="mode_sel" value="--careful"/> | |
233 <param name="optional_output" value="l"/> | |
234 <output name="out_l"> | |
235 <assert_contents> | |
236 <has_text_matching expression="Thank you for using SPAdes!"/> | |
237 </assert_contents> | |
238 </output> | |
239 </test> | |
240 <!-- #5 only corrected reads are created as an output --> | |
241 <test expect_num_outputs="2"> | |
242 <param name="operation_mode" value="--only-error-correction"/> | |
243 <conditional name="singlePaired"> | |
244 <param name="sPaired" value="paired"/> | |
245 <param name="input1" value="pl1.fq.gz"/> | |
246 <param name="input2" value="pl2.fq.gz"/> | |
247 </conditional> | |
248 <param name="optional_output" value="cr,l"/> | |
249 <output_collection name="out_cr" type="list" count="3"> | |
250 <element name="pl1.fq.gz.fastq.00.0_0.cor"> | |
251 <assert_contents> | |
252 <has_size value="72173" delta="1000"/> | |
253 </assert_contents> | |
254 </element> | |
255 <element name="pl2.fq.gz.fastq.00.0_0.cor"> | |
256 <assert_contents> | |
257 <has_size value="72173" delta="1000"/> | |
258 </assert_contents> | |
259 </element> | |
260 <element name="pl_unpaired.00.0_0.cor"> | |
261 <assert_contents> | |
262 <has_size value="392" delta="100"/> | |
263 </assert_contents> | |
264 </element> | |
265 </output_collection> | |
266 <output name="out_l"> | |
267 <assert_contents> | |
268 <has_text_matching expression="Thank you for using SPAdes!"/> | |
269 </assert_contents> | |
270 </output> | |
271 </test> | |
272 <!-- #6 only corrected reads are created as an output --> | |
273 <test expect_num_outputs="2"> | |
274 <param name="operation_mode" value="--only-error-correction"/> | |
275 <conditional name="singlePaired"> | |
276 <param name="sPaired" value="paired"/> | |
277 <param name="input1" value="pl1.fq.gz"/> | |
278 <param name="input2" value="pl2.fq.gz"/> | |
279 </conditional> | |
280 <param name="optional_output" value="cr,l"/> | |
281 <output_collection name="out_cr" type="list" count="3"> | |
282 <element name="pl1.fq.gz.fastq.00.0_0.cor"> | |
283 <assert_contents> | |
284 <has_size value="72173" delta="1000"/> | |
285 </assert_contents> | |
286 </element> | |
287 <element name="pl2.fq.gz.fastq.00.0_0.cor"> | |
288 <assert_contents> | |
289 <has_size value="72173" delta="1000"/> | |
290 </assert_contents> | |
291 </element> | |
292 <element name="pl_unpaired.00.0_0.cor"> | |
293 <assert_contents> | |
294 <has_size value="392" delta="100"/> | |
295 </assert_contents> | |
296 </element> | |
297 </output_collection> | |
298 <output name="out_l"> | |
299 <assert_contents> | |
300 <has_text_matching expression="Thank you for using SPAdes!"/> | |
301 </assert_contents> | |
302 </output> | |
303 </test> | |
304 <!-- #7 hybrid assembly: nanpopore, pacbio, sanger, untrustedcontigs --> | |
305 <test expect_num_outputs="2"> | |
306 <conditional name="singlePaired"> | |
307 <param name="sPaired" value="paired"/> | |
308 <param name="input1" value="pl1.fq.gz"/> | |
309 <param name="input2" value="pl2.fq.gz"/> | |
310 </conditional> | |
311 <section name="arf"> | |
312 <param name="nanopore" value="ecoli_1K.fastq.gz"/> | |
313 <param name="pacbio" value="ecoli_1K.fastq.gz"/> | |
314 <param name="sanger" value="ecoli_1K.fastq.gz"/> | |
315 <param name="untrusted_contigs" value="ecoli_1K.fasta.gz"/> | |
316 </section> | |
317 <assert_command> | |
318 <has_text text="--nanopore"/> | |
319 <has_text text="--pacbio"/> | |
320 <has_text text="--sanger"/> | |
321 <has_text text="--untrusted-contigs"/> | |
322 </assert_command> | |
323 <param name="mode_sel" value="--careful"/> | |
324 <param name="optional_output" value="cr,l"/> | |
325 <output_collection name="out_cr" type="list" count="3"> | |
326 <element name="pl1.fq.gz.fastq.00.0_0.cor"> | |
327 <assert_contents> | |
328 <has_size value="72173" delta="1000"/> | |
329 </assert_contents> | |
330 </element> | |
331 <element name="pl2.fq.gz.fastq.00.0_0.cor"> | |
332 <assert_contents> | |
333 <has_size value="72173" delta="1000"/> | |
334 </assert_contents> | |
335 </element> | |
336 <element name="pl_unpaired.00.0_0.cor"> | |
337 <assert_contents> | |
338 <has_size value="392" delta="100"/> | |
339 </assert_contents> | |
340 </element> | |
341 </output_collection> | |
342 <output name="out_l"> | |
343 <assert_contents> | |
344 <has_text_matching expression="Thank you for using SPAdes!"/> | |
345 </assert_contents> | |
346 </output> | |
347 </test> | |
348 </tests> | |
349 <help><![CDATA[ | |
350 .. class:: infomark | |
351 | |
352 **What it does** | |
353 | |
354 @HELP_WID@ | |
355 | |
356 plasmidSPAdes is a subtool for assembling plasmid data sets. | |
357 | |
358 **Input** | |
359 | |
360 @HELP_IN@ | |
361 | |
362 **Output** | |
363 | |
364 @HELP_OUT_AG@ | |
365 @HELP_OUT_AGS@ | |
366 @HELP_OUT_C@ | |
367 @HELP_OUT_CP@ | |
368 @HELP_OUT_CR@ | |
369 @HELP_OUT_CS@ | |
370 @HELP_OUT_L@ | |
371 @HELP_OUT_S@ | |
372 @HELP_OUT_SP@ | |
373 @HELP_OUT_SS@ | |
374 | |
375 **References** | |
376 | |
377 More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/plasmid-spades>`_. | |
378 ]]></help> | |
379 <expand macro="citations"> | |
380 <citation type="doi">10.1093/bioinformatics/btw493</citation> | |
381 </expand> | |
382 </tool> |