Mercurial > repos > iuc > semibin_generate_sequence_features

comparison generate_sequence_features.xml @ 5:8ba0c2edf3f3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
author iuc
date Sun, 10 Aug 2025 11:39:49 +0000
parents 0608cf7dc528
children
comparison
equal deleted inserted replaced
4:40ffba87bbcf 5:8ba0c2edf3f3
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 $input_type_select.mode.select == 'co'
18 generate_sequence_features_single 25 generate_sequence_features_single
19 #else 26 #else
20 generate_sequence_features_multi 27 generate_sequence_features_multi
21 --separator '$separator' 28 --separator '$separator'
22 #end if 29 #end if
23 --input-fasta 'contigs.fasta' 30 --input-fasta 'contigs.fasta'
31 #if $input_type_select.input_type == "bam"
24 --input-bam *.bam 32 --input-bam *.bam
33 #else:
34 -a *.txt
35 #end if
25 --output 'output' 36 --output 'output'
26 --threads \${GALAXY_SLOTS:-1} 37 --threads \${GALAXY_SLOTS:-1}
27 @MIN_LEN@ 38 @MIN_LEN@
28 #if $ml_threshold: 39 #if $ml_threshold:
29 --ml-threshold $ml_threshold 40 --ml-threshold $ml_threshold
30 #end if 41 #end if
31 ]]></command> 42 ]]></command>
32 <inputs> 43 <inputs>
33 <expand macro="mode_fasta_bam"/> 44 <conditional name="input_type_select">
45 <param name="input_type" type="select" label="Use BAM or strobealign abundance information?">
46 <option value="bam">BAM file</option>
47 <option value="txt">strobealign-aemb files</option>
48 </param>
49 <when value="bam">
50 <expand macro="mode_fasta_bam"/>
51 </when>
52 <when value="txt">
53 <expand macro="mode_fasta_strobealign"/>
54 </when>
55 </conditional>
34 <expand macro="min_len"/> 56 <expand macro="min_len"/>
35 <expand macro="ml-threshold"/> 57 <expand macro="ml-threshold"/>
36 <param name="extra_output" type="select" multiple="true" label="Extra outputs" help="In addition to the training data"> 58 <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> 59 <option value="coverage">Coverage files</option>
38 <option value="contigs">Contigs (if multiple sample)</option> 60 <option value="contigs">Contigs (if multiple sample)</option>
43 <expand macro="data_output_multi"/> 65 <expand macro="data_output_multi"/>
44 <expand macro="generate_sequence_features_extra_outputs"/> 66 <expand macro="generate_sequence_features_extra_outputs"/>
45 </outputs> 67 </outputs>
46 <tests> 68 <tests>
47 <test expect_num_outputs="4"> 69 <test expect_num_outputs="4">
48 <conditional name="mode"> 70 <conditional name="input_type_select">
49 <param name="select" value="single"/> 71 <param name="input_type" value="bam"/>
50 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 72 <conditional name="mode">
51 <param name="input_bam" ftype="bam" value="input_single.bam"/> 73 <param name="select" value="single"/>
74 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
75 <param name="input_bam" ftype="bam" value="input_single.bam"/>
76 </conditional>
52 </conditional> 77 </conditional>
53 <conditional name="min_len"> 78 <conditional name="min_len">
54 <param name="method" value="automatic"/> 79 <param name="method" value="automatic"/>
55 </conditional> 80 </conditional>
56 <param name="ml_threshold" value="4000"/> 81 <param name="ml_threshold" value="4000"/>
81 <has_n_lines n="1" delta="1"/> 106 <has_n_lines n="1" delta="1"/>
82 </assert_contents> 107 </assert_contents>
83 </output> 108 </output>
84 </test> 109 </test>
85 <test expect_num_outputs="4"> 110 <test expect_num_outputs="4">
86 <conditional name="mode"> 111 <conditional name="input_type_select">
87 <param name="select" value="co"/> 112 <param name="input_type" value="bam"/>
88 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> 113 <conditional name="mode">
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"/> 114 <param name="select" value="co"/>
115 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
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"/>
136 </assert_contents> 164 </assert_contents>
137 </element> 165 </element>
138 </output_collection> 166 </output_collection>
139 </test> 167 </test>
140 <test expect_num_outputs="7"> 168 <test expect_num_outputs="7">
141 <conditional name="mode"> 169 <conditional name="input_type_select">
142 <param name="select" value="multi"/> 170 <param name="input_type" value="bam"/>
143 <conditional name="multi_fasta"> 171 <conditional name="mode">
144 <param name="select" value="concatenated"/> 172 <param name="select" value="multi"/>
145 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/> 173 <conditional name="multi_fasta">
146 </conditional> 174 <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"/> 175 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
176 </conditional>
177 <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"/>
178 </conditional>
148 </conditional> 179 </conditional>
149 <conditional name="min_len"> 180 <conditional name="min_len">
150 <param name="method" value="automatic"/> 181 <param name="method" value="automatic"/>
151 </conditional> 182 </conditional>
152 <param name="ml_threshold" value="4000"/> 183 <param name="ml_threshold" value="4000"/>
222 <has_text text=">g1k_0"/> 253 <has_text text=">g1k_0"/>
223 </assert_contents> 254 </assert_contents>
224 </element> 255 </element>
225 </output_collection> 256 </output_collection>
226 </test> 257 </test>
258
259 <test expect_num_outputs="5">
260 <conditional name="input_type_select">
261 <param name="input_type" value="txt"/>
262 <conditional name="mode">
263 <param name="select" value="multi"/>
264 <conditional name="multi_fasta">
265 <param name="select" value="concatenated"/>
266 <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/>
267 </conditional>
268 <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/>
269 </conditional>
270 </conditional>
271 <conditional name="min_len">
272 <param name="method" value="automatic"/>
273 </conditional>
274 <param name="ml_threshold" value="4000"/>
275 <param name="extra_output" value="coverage,contigs"/>
276 <output_collection name="multi_data" count="10">
277 <element name="S1" ftype="csv">
278 <assert_contents>
279 <has_n_lines n="21"/>
280 <has_text text="g1k_0"/>
281 </assert_contents>
282 </element>
283 </output_collection>
284 <output_collection name="multi_data_split" count="10">
285 <element name="S1" ftype="csv">
286 <assert_contents>
287 <has_n_lines n="41"/>
288 <has_text text="g1k_0_1"/>
289 </assert_contents>
290 </element>
291 </output_collection>
292 <output_collection name="multi_cov_sample" count="10">
293 <element name="S1" ftype="csv">
294 <assert_contents>
295 <has_n_lines n="21"/>
296 <has_text text="g1k_0"/>
297 </assert_contents>
298 </element>
299 </output_collection>
300 <output_collection name="multi_split_cov_txt" count="10">
301 <element name="S1" ftype="csv">
302 <assert_contents>
303 <has_n_lines n="41"/>
304 <has_text text="g1k_5_1"/>
305 </assert_contents>
306 </element>
307 <element name="S9" ftype="csv">
308 <assert_contents>
309 <has_n_lines n="41"/>
310 <has_text text="g1k_5_1"/>
311 </assert_contents>
312 </element>
313 </output_collection>
314 <output_collection name="multi_contigs" count="10">
315 <element name="S1" ftype="fasta">
316 <assert_contents>
317 <has_text text=">g1k_0"/>
318 </assert_contents>
319 </element>
320 <element name="S9" ftype="fasta">
321 <assert_contents>
322 <has_text text=">g1k_0"/>
323 </assert_contents>
324 </element>
325 </output_collection>
326 </test>
327
227 <test expect_num_outputs="2"> 328 <test expect_num_outputs="2">
228 <conditional name="mode"> 329 <conditional name="input_type_select">
229 <param name="select" value="multi"/> 330 <param name="input_type" value="bam"/>
230 <conditional name="multi_fasta"> 331 <conditional name="mode">
231 <param name="select" value="multi"/> 332 <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"/> 333 <conditional name="multi_fasta">
233 </conditional> 334 <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"/> 335 <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"/>
336 </conditional>
337 <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"/>
338 </conditional>
235 </conditional> 339 </conditional>
236 <conditional name="min_len"> 340 <conditional name="min_len">
237 <param name="method" value="automatic"/> 341 <param name="method" value="automatic"/>
238 </conditional> 342 </conditional>
239 <param name="ml_threshold" value="4000"/> 343 <param name="ml_threshold" value="4000"/>