Mercurial > repos > iuc > semibin_generate_sequence_features

comparison generate_sequence_features.xml @ 3:b55f0ce54d97 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
author iuc
date Tue, 28 Oct 2025 08:16:56 +0000
parents f5aff7c9a65d
children
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2:f5aff7c9a65d 3:b55f0ce54d97
8 <expand macro="biotools"/> 8 <expand macro="biotools"/>
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="version"/> 10 <expand macro="version"/>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #import re 12 #import re
13 @BAM_FILES@ 13 #if $input_type_select.input_type == "bam":
14 @BAM_FILES@
15 #else:
16 #for $e in $input_type_select.mode.abundance:
17 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
18 ln -s '$e' '${identifier}.txt' &&
19 #end for
20 #end if
14 @FASTA_FILES@ 21 @FASTA_FILES@
15 22
16 SemiBin2 23 SemiBin2
17 #if $mode.select == 'single' or $mode.select == 'co' 24 #if $input_type_select.mode.select == 'single' or $input_type_select.mode.select == 'co'
18 generate_sequence_features_single 25 generate_sequence_features_single
26 --input-fasta 'contigs.$input_fasta.ext'
19 #else 27 #else
20 generate_sequence_features_multi 28 generate_sequence_features_multi
21 --separator '$separator' 29 --separator '$separator'
30 --input-fasta 'contigs.fasta'
22 #end if 31 #end if
23 --input-fasta 'contigs.fasta' 32 #if $input_type_select.input_type == "bam"
24 --input-bam *.bam 33 --input-bam *.bam
34 #else:
35 -a *.txt
36 #end if
25 --output 'output' 37 --output 'output'
26 --threads \${GALAXY_SLOTS:-1} 38 --threads \${GALAXY_SLOTS:-1}
27 @MIN_LEN@ 39 @MIN_LEN@
28 #if $ml_threshold: 40 #if $ml_threshold:
29 --ml-threshold $ml_threshold 41 --ml-threshold $ml_threshold
30 #end if 42 #end if
31 ]]></command> 43 ]]></command>
32 <inputs> 44 <inputs>
33 <expand macro="mode_fasta_bam"/> 45 <conditional name="input_type_select">
46 <param name="input_type" type="select" label="Use BAM or strobealign abundance information?">
47 <option value="bam">BAM file</option>
48 <option value="txt">strobealign-aemb files</option>
49 </param>
50 <when value="bam">
51 <expand macro="mode_fasta_bam"/>
52 </when>
53 <when value="txt">
54 <expand macro="mode_fasta_strobealign"/>
55 </when>
56 </conditional>
34 <expand macro="min_len"/> 57 <expand macro="min_len"/>
35 <expand macro="ml-threshold"/> 58 <expand macro="ml-threshold"/>
36 <param name="extra_output" type="select" multiple="true" label="Extra outputs" help="In addition to the training data"> 59 <param name="extra_output" type="select" multiple="true" label="Extra outputs" help="In addition to the training data">
37 <option value="coverage">Coverage files</option> 60 <option value="coverage">Coverage files</option>
38 <option value="contigs">Contigs (if multiple sample)</option> 61 <option value="contigs">Contigs (if multiple sample)</option>
43 <expand macro="data_output_multi"/> 66 <expand macro="data_output_multi"/>
44 <expand macro="generate_sequence_features_extra_outputs"/> 67 <expand macro="generate_sequence_features_extra_outputs"/>
45 </outputs> 68 </outputs>
46 <tests> 69 <tests>
47 <test expect_num_outputs="4"> 70 <test expect_num_outputs="4">
48 <conditional name="mode"> 71 <conditional name="input_type_select">
49 <param name="select" value="single"/> 72 <param name="input_type" value="bam"/>
50 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 73 <conditional name="mode">
51 <param name="input_bam" ftype="bam" value="input_single.bam"/> 74 <param name="select" value="single"/>
75 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
76 <param name="input_bam" ftype="bam" value="input_single.bam"/>
77 </conditional>
52 </conditional> 78 </conditional>
53 <conditional name="min_len"> 79 <conditional name="min_len">
54 <param name="method" value="automatic"/> 80 <param name="method" value="automatic"/>
55 </conditional> 81 </conditional>
56 <param name="ml_threshold" value="4000"/> 82 <param name="ml_threshold" value="4000"/>
79 <output name="single_split_cov" ftype="csv"> 105 <output name="single_split_cov" ftype="csv">
80 <assert_contents> 106 <assert_contents>
81 <has_n_lines n="1" delta="1"/> 107 <has_n_lines n="1" delta="1"/>
82 </assert_contents> 108 </assert_contents>
83 </output> 109 </output>
84 </test> 110 </test><test expect_num_outputs="4">
85 <test expect_num_outputs="4"> 111 <conditional name="input_type_select">
86 <conditional name="mode"> 112 <param name="input_type" value="bam"/>
87 <param name="select" value="co"/> 113 <conditional name="mode">
88 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 114 <param name="select" value="co"/>
89 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/> 115 <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
116 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
117 </conditional>
90 </conditional> 118 </conditional>
91 <conditional name="min_len"> 119 <conditional name="min_len">
92 <param name="method" value="automatic"/> 120 <param name="method" value="automatic"/>
93 </conditional> 121 </conditional>
94 <param name="ml_threshold" value="4000"/> 122 <param name="ml_threshold" value="4000"/>
135 <has_text text="g1k_0_1"/> 163 <has_text text="g1k_0_1"/>
136 </assert_contents> 164 </assert_contents>
137 </element> 165 </element>
138 </output_collection> 166 </output_collection>
139 </test> 167 </test>
168 <test expect_num_outputs="4">
169 <conditional name="input_type_select">
170 <param name="input_type" value="bam"/>
171 <conditional name="mode">
172 <param name="select" value="co"/>
173 <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
174 <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/>
175 </conditional>
176 </conditional>
177 <conditional name="min_len">
178 <param name="method" value="automatic"/>
179 </conditional>
180 <param name="ml_threshold" value="4000"/>
181 <param name="extra_output" value="coverage"/>
182 <output name="single_data" ftype="csv">
183 <assert_contents>
184 <has_n_lines n="41"/>
185 <has_text text="g1k_0"/>
186 <has_text text="g4k_9"/>
187 </assert_contents>
188 </output>
189 <output name="single_data_split" ftype="csv">
190 <assert_contents>
191 <has_n_lines n="81"/>
192 <has_text text="g1k_0_1"/>
193 <has_text text="g3k_2_2"/>
194 <has_text text="g4k_7_2"/>
195 </assert_contents>
196 </output>
197 <output_collection name="co_cov" count="5">
198 <element name="0" ftype="csv">
199 <assert_contents>
200 <has_n_lines n="41"/>
201 <has_text text="g1k_0"/>
202 </assert_contents>
203 </element>
204 <element name="4" ftype="csv">
205 <assert_contents>
206 <has_n_lines n="41"/>
207 <has_text text="g1k_0"/>
208 </assert_contents>
209 </element>
210 </output_collection>
211 <output_collection name="co_split_cov" count="5">
212 <element name="0" ftype="csv">
213 <assert_contents>
214 <has_n_lines n="81"/>
215 <has_text text="g1k_0_1"/>
216 </assert_contents>
217 </element>
218 <element name="4" ftype="csv">
219 <assert_contents>
220 <has_n_lines n="81"/>
221 <has_text text="g1k_0_1"/>
222 </assert_contents>
223 </element>
224 </output_collection>
225 </test>
140 <test expect_num_outputs="7"> 226 <test expect_num_outputs="7">
141 <conditional name="mode"> 227 <conditional name="input_type_select">
142 <param name="select" value="multi"/> 228 <param name="input_type" value="bam"/>
143 <conditional name="multi_fasta"> 229 <conditional name="mode">
144 <param name="select" value="concatenated"/> 230 <param name="select" value="multi"/>
145 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/> 231 <conditional name="multi_fasta">
146 </conditional> 232 <param name="select" value="concatenated"/>
147 <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/> 233 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
234 </conditional>
235 <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/>
236 </conditional>
148 </conditional> 237 </conditional>
149 <conditional name="min_len"> 238 <conditional name="min_len">
150 <param name="method" value="automatic"/> 239 <param name="method" value="automatic"/>
151 </conditional> 240 </conditional>
152 <param name="ml_threshold" value="4000"/> 241 <param name="ml_threshold" value="4000"/>
222 <has_text text=">g1k_0"/> 311 <has_text text=">g1k_0"/>
223 </assert_contents> 312 </assert_contents>
224 </element> 313 </element>
225 </output_collection> 314 </output_collection>
226 </test> 315 </test>
316
317 <test expect_num_outputs="5">
318 <conditional name="input_type_select">
319 <param name="input_type" value="txt"/>
320 <conditional name="mode">
321 <param name="select" value="multi"/>
322 <conditional name="multi_fasta">
323 <param name="select" value="concatenated"/>
324 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
325 </conditional>
326 <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
327 </conditional>
328 </conditional>
329 <conditional name="min_len">
330 <param name="method" value="automatic"/>
331 </conditional>
332 <param name="ml_threshold" value="4000"/>
333 <param name="extra_output" value="coverage,contigs"/>
334 <output_collection name="multi_data" count="10">
335 <element name="S1" ftype="csv">
336 <assert_contents>
337 <has_n_lines n="21"/>
338 <has_text text="g1k_0"/>
339 </assert_contents>
340 </element>
341 </output_collection>
342 <output_collection name="multi_data_split" count="10">
343 <element name="S1" ftype="csv">
344 <assert_contents>
345 <has_n_lines n="41"/>
346 <has_text text="g1k_0_1"/>
347 </assert_contents>
348 </element>
349 </output_collection>
350 <output_collection name="multi_cov_sample" count="10">
351 <element name="S1" ftype="csv">
352 <assert_contents>
353 <has_n_lines n="21"/>
354 <has_text text="g1k_0"/>
355 </assert_contents>
356 </element>
357 </output_collection>
358 <output_collection name="multi_split_cov_txt" count="10">
359 <element name="S1" ftype="csv">
360 <assert_contents>
361 <has_n_lines n="41"/>
362 <has_text text="g1k_5_1"/>
363 </assert_contents>
364 </element>
365 <element name="S9" ftype="csv">
366 <assert_contents>
367 <has_n_lines n="41"/>
368 <has_text text="g1k_5_1"/>
369 </assert_contents>
370 </element>
371 </output_collection>
372 <output_collection name="multi_contigs" count="10">
373 <element name="S1" ftype="fasta">
374 <assert_contents>
375 <has_text text=">g1k_0"/>
376 </assert_contents>
377 </element>
378 <element name="S9" ftype="fasta">
379 <assert_contents>
380 <has_text text=">g1k_0"/>
381 </assert_contents>
382 </element>
383 </output_collection>
384 </test>
227 <test expect_num_outputs="2"> 385 <test expect_num_outputs="2">
228 <conditional name="mode"> 386 <conditional name="input_type_select">
229 <param name="select" value="multi"/> 387 <param name="input_type" value="bam"/>
230 <conditional name="multi_fasta"> 388 <conditional name="mode">
231 <param name="select" value="multi"/> 389 <param name="select" value="multi"/>
232 <param name="input_fasta" ftype="fasta" value="S1.fasta,S2.fasta,S3.fasta,S4.fasta,S5.fasta,S6.fasta,S7.fasta,S8.fasta,S9.fasta,S10.fasta"/> 390 <conditional name="multi_fasta">
233 </conditional> 391 <param name="select" value="multi"/>
234 <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/> 392 <param name="input_fasta" ftype="fasta" value="S1.fasta,S2.fasta,S3.fasta,S4.fasta,S5.fasta,S6.fasta,S7.fasta,S8.fasta,S9.fasta,S10.fasta"/>
393 </conditional>
394 <param name="input_bam" ftype="bam" value="input_multi_sorted1_naming.bam,input_multi_sorted2_naming.bam,input_multi_sorted3_naming.bam,input_multi_sorted4_naming.bam,input_multi_sorted5_naming.bam,input_multi_sorted6_naming.bam,input_multi_sorted7_naming.bam,input_multi_sorted8_naming.bam,input_multi_sorted9_naming.bam,input_multi_sorted10_naming.bam"/>
395 </conditional>
235 </conditional> 396 </conditional>
236 <conditional name="min_len"> 397 <conditional name="min_len">
237 <param name="method" value="automatic"/> 398 <param name="method" value="automatic"/>
238 </conditional> 399 </conditional>
239 <param name="ml_threshold" value="4000"/> 400 <param name="ml_threshold" value="4000"/>
240 <output_collection name="multi_data" count="10"> 401 <output_collection name="multi_data" count="10">
241 <element name="S1" ftype="csv"> 402 <element name="S1_fasta" ftype="csv">
242 <assert_contents> 403 <assert_contents>
243 <has_n_lines n="21"/> 404 <has_n_lines n="21"/>
244 <has_text text="g1k_0"/> 405 <has_text text="g1k_0"/>
245 </assert_contents> 406 </assert_contents>
246 </element> 407 </element>
247 </output_collection> 408 </output_collection>
248 <output_collection name="multi_data_split" count="10"> 409 <output_collection name="multi_data_split" count="10">
249 <element name="S1" ftype="csv"> 410 <element name="S1_fasta" ftype="csv">
250 <assert_contents> 411 <assert_contents>
251 <has_n_lines n="41"/> 412 <has_n_lines n="41"/>
252 <has_text text="g1k_0_1"/> 413 <has_text text="g1k_0_1"/>
253 </assert_contents> 414 </assert_contents>
254 </element> 415 </element>