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comparison rnaviralspades.xml @ 0:5df83f4bad67 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 21:31:52 +0000
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children 249f6a28c751
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-1:000000000000 0:5df83f4bad67
1 <tool id="spades_rnaviralspades" name="rnaviralSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>de novo assembler for transcriptomes, metatranscriptomes and metaviromes</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_CONTIGS_FILES@
19 @PREPROCESS_SANGER_FILES@
20
21 ## run
22 spades.py --rnaviral
23 -o 'output'
24 @RESOURCES@
25 @INPUT_READS_MAIN@
26 #if $additional_reads.selector == 'true'
27 @INPUT_READS_ADDITIONAL@
28 #end if
29 ## additional reads
30 @NANOPORE_PACBIO@
31 @SANGER@
32 @CONTIGS@
33 ## parameter
34 @KMER@
35 @PIPELINE_OPTIONS@
36 @PHREDOFFSET@
37
38 ## postprocessing
39 @STATS@
40 @CORRECTED@
41 ]]></command>
42 <inputs>
43 <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/>
44 <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/>
45 <section name="arf" title="Additional read files">
46 <expand macro="sanger"/>
47 <expand macro="nanopore_pacbio"/>
48 <expand macro="contigs"/>
49 </section>
50 <expand macro="pipeline_options">
51 <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option>
52 </expand>
53 <expand macro="kmer" help="By default rnaSPAdes uses 2 k-mer sizes, which are automatically detected using read length (approximately one third and half of the maximal read length). We recommend not to change this parameter because smaller k-mer sizes typically result in multiple chimeric (misassembled) transcripts."/>
54 <expand macro="phred"/>
55 <expand macro="optional_output"/>
56 </inputs>
57 <outputs>
58 <expand macro="out_ag"/>
59 <expand macro="out_ags"/>
60 <expand macro="out_cn"/>
61 <expand macro="out_cp"/>
62 <expand macro="out_cr"/>
63 <expand macro="out_cs"/>
64 <expand macro="out_l"/>
65 <expand macro="out_sc"/>
66 <expand macro="out_sp"/>
67 <expand macro="out_ss"/>
68 </outputs>
69 <tests>
70 <!--
71 used in a test:
72 single library: 12, 1, 2
73 multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or>
74 k, phred-offset, disablerr, iontorrent, careful, isolate, only-assembler, only-error-correction, sc
75
76 not used in a test:
77 single library: merged, s
78 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
79 pacbio, nanopore, sanger, trusted-contigs, untrusted-contigs, tslr
80 -->
81
82 <!-- #1 single, interlaced, fastq.gz, default parameters -->
83 <test expect_num_outputs="4">
84 <conditional name="singlePaired">
85 <param name="sPaired" value="paired_interlaced"/>
86 <param name="input1" value="ecoli_1K.fastq.gz"/>
87 </conditional>
88 <output name="out_ag">
89 <assert_contents>
90 <has_n_lines n="36"/>
91 <has_text_matching expression=">EDGE\_3\_length.+"/>
92 </assert_contents>
93 </output>
94 <output name="out_ags">
95 <assert_contents>
96 <has_n_lines n="2"/>
97 <has_text_matching expression="S.+"/>
98 </assert_contents>
99 </output>
100 <output name="out_cn">
101 <assert_contents>
102 <has_n_lines n="18"/>
103 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
104 </assert_contents>
105 </output>
106 <output name="out_sc">
107 <assert_contents>
108 <has_n_lines n="18"/>
109 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
110 </assert_contents>
111 </output>
112 </test>
113 <!-- #2 single, separate, fastq, all outputs -->
114 <test expect_num_outputs="10">
115 <conditional name="singlePaired">
116 <param name="sPaired" value="paired"/>
117 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
118 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
119 </conditional>
120 <conditional name="cov_cond">
121 <param name="cov_cutoff" value="auto"/>
122 </conditional>
123 <param name="mode_sel" value="--disable-rr,--iontorrent"/>
124 <param name="phred_offset" value="33"/>
125 <param name="optional_output" value="ag,ags,cn,cp,cs,cr,sc,sp,ss,l"/>
126 <output name="out_ag">
127 <assert_contents>
128 <has_n_lines n="36"/>
129 <has_text_matching expression=">EDGE.+"/>
130 </assert_contents>
131 </output>
132 <output name="out_ags">
133 <assert_contents>
134 <has_n_lines n="1"/>
135 <has_text_matching expression="S.+"/>
136 </assert_contents>
137 </output>
138 <output name="out_cn">
139 <assert_contents>
140 <has_n_lines n="18"/>
141 <has_text_matching expression=">NODE.+"/>
142 </assert_contents>
143 </output>
144 <output name="out_cp">
145 <assert_contents>
146 <has_n_lines n="0"/>
147 </assert_contents>
148 </output>
149 <output_collection name="out_cr" type="list" count="2">
150 <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor">
151 <assert_contents>
152 <has_size value="34468" delta="1000"/>
153 </assert_contents>
154 </element>
155 <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor">
156 <assert_contents>
157 <has_size value="34468" delta="1000"/>
158 </assert_contents>
159 </element>
160 </output_collection>
161 <output name="out_cs">
162 <assert_contents>
163 <has_n_lines n="1"/>
164 <has_text_matching expression="#name&#009;length&#009;coverage"/>
165 </assert_contents>
166 </output>
167 <output name="out_l">
168 <assert_contents>
169 <has_text_matching expression="Thank you for using SPAdes!"/>
170 </assert_contents>
171 </output>
172 <output name="out_sc">
173 <assert_contents>
174 <has_n_lines n="0"/>
175 </assert_contents>
176 </output>
177 <output name="out_sp">
178 <assert_contents>
179 <has_n_lines n="0"/>
180 </assert_contents>
181 </output>
182 <output name="out_ss">
183 <assert_contents>
184 <has_n_lines n="0"/>
185 </assert_contents>
186 </output>
187 </test>
188 <!-- #3 single, separate, fasta, default parameters -->
189 <test expect_num_outputs="4">
190 <conditional name="singlePaired">
191 <param name="sPaired" value="paired"/>
192 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
193 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
194 </conditional>
195 <output name="out_ag">
196 <assert_contents>
197 <has_n_lines n="36"/>
198 <has_text_matching expression=">EDGE_3_length_1000_cov_163.370137"/>
199 </assert_contents>
200 </output>
201 <output name="out_ags">
202 <assert_contents>
203 <has_n_lines n="2"/>
204 <has_text_matching expression="S.+"/>
205 </assert_contents>
206 </output>
207 <output name="out_cn">
208 <assert_contents>
209 <has_n_lines n="18"/>
210 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
211 </assert_contents>
212 </output>
213 <output name="out_sc">
214 <assert_contents>
215 <has_n_lines n="18"/>
216 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
217 </assert_contents>
218 </output>
219 </test>
220 <!-- #4 multiple, single & paired-end-->
221 <test expect_num_outputs="4">
222 <param name="operation_mode" value="--only-assembler"/>
223 <conditional name="singlePaired">
224 <param name="sPaired" value="single"/>
225 <param name="input1" value="ecoli_1K.fastq.gz"/>
226 </conditional>
227 <conditional name="additional_reads">
228 <param name="selector" value="true"/>
229 <conditional name="singlePaired">
230 <param name="sPaired" value="paired"/>
231 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
232 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
233 </conditional>
234 </conditional>
235 <section name="arf">
236 <param name="nanopore" value="ecoli_1K.fastq.gz"/>
237 <param name="pacbio" value="ecoli_1K.fastq.gz"/>
238 <param name="sanger" value="ecoli_1K.fastq.gz"/>
239 <param name="trusted_contigs" value="ecoli_1K.fasta.gz"/>
240 </section>
241 <assert_command>
242 <has_text text="--nanopore"/>
243 <has_text text="--pacbio"/>
244 <has_text text="--sanger"/>
245 <has_text text="--trusted-contigs"/>
246 </assert_command>
247 <output name="out_ag">
248 <assert_contents>
249 <has_n_lines n="36"/>
250 <has_text_matching expression=">EDGE_.+"/>
251 </assert_contents>
252 </output>
253 <output name="out_ags">
254 <assert_contents>
255 <has_n_lines n="2"/>
256 <has_text_matching expression="S.+"/>
257 </assert_contents>
258 </output>
259 <output name="out_cn">
260 <assert_contents>
261 <has_n_lines n="18"/>
262 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
263 </assert_contents>
264 </output>
265 <output name="out_sc">
266 <assert_contents>
267 <has_n_lines n="18"/>
268 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
269 </assert_contents>
270 </output>
271 </test>
272 <!-- #5 Multiple samples, different libraries: hybrid assembly: nanopore, pacbio -->
273 <test expect_num_outputs="4">
274 <param name="operation_mode" value="--only-assembler"/>
275 <conditional name="singlePaired">
276 <param name="sPaired" value="single"/>
277 <param name="input1" value="ecoli_1K.fastq.gz"/>
278 </conditional>
279 <conditional name="additional_reads">
280 <param name="selector" value="true"/>
281 <conditional name="singlePaired">
282 <param name="sPaired" value="paired"/>
283 <param name="input1" value="ecoli_1K_1.fastq.gz"/>
284 <param name="input2" value="ecoli_1K_2.fastq.gz"/>
285 </conditional>
286 <param name="library_number" value="false"/>
287 </conditional>
288
289 <output name="out_ag">
290 <assert_contents>
291 <has_n_lines n="36"/>
292 <has_text_matching expression=">EDGE_3_length_1000_cov_326.740273"/>
293 </assert_contents>
294 </output>
295 <output name="out_ags">
296 <assert_contents>
297 <has_n_lines n="2"/>
298 <has_text_matching expression="S.+"/>
299 </assert_contents>
300 </output>
301 <output name="out_cn">
302 <assert_contents>
303 <has_n_lines n="18"/>
304 <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/>
305 </assert_contents>
306 </output>
307 <output name="out_sc">
308 <assert_contents>
309 <has_n_lines n="18"/>
310 <has_text_matching expression=">NODE\_1\_length\_1000.+"/>
311 </assert_contents>
312 </output>
313 </test>
314 </tests>
315 <help><![CDATA[
316 .. class:: infomark
317
318 **What it does**
319
320 @HELP_WID@
321
322 rnaviralSPAdes is a pipeline specially designed for de novo assembler tailored for RNA viral datasets (transcriptome, metatranscriptome and metavirome).
323
324 **Input**
325
326 @HELP_IN@
327
328 **Output**
329
330 @HELP_OUT_AG@
331 @HELP_OUT_AGS@
332 @HELP_OUT_C@
333 @HELP_OUT_CP@
334 @HELP_OUT_CR@
335 @HELP_OUT_CS@
336 @HELP_OUT_L@
337 @HELP_OUT_S@
338 @HELP_OUT_SP@
339 @HELP_OUT_SS@
340
341
342 -------------------
343
344 .. class:: infomark
345
346 **IonTorrent data**
347
348 @IONTORRENT@
349
350 -------------------
351
352 .. class:: infomark
353
354 **References**
355
356 More information are available on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_.
357 ]]></help>
358 <expand macro="citations"/>
359 </tool>