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comparison plasmidspades.xml @ 0:eabeb1a74dac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author iuc
date Sun, 23 Jan 2022 21:32:59 +0000
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children 6aad515a5270
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-1:000000000000 0:eabeb1a74dac
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&#009;length&#009;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>