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planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 0ee665c3393af083833fdb9becbe6965d009e16c
author iuc
date Sat, 09 Nov 2024 13:53:38 +0000
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1 <tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
2 <description>Construct robust assemblies of highly variable RNA viruses</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">irma-virus</xref>
9 </xrefs>
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">irma</requirement>
12 <requirement type="package" version="3.12">python</requirement>
13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[
15 ## handle gz inputs
16 #if $input_type == 'single'
17 #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
18 ln -sf '${input_type_conditional.fastq_input1}' file1.fastq.gz &&
19 #end if
20 #elif $input_type == 'paired_collection'
21 #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
22 ln -sf '${input_type_conditional.fastq_input.forward}' file1.fastq.gz &&
23 ln -sf '${input_type_conditional.fastq_input.reverse}' file2.fastq.gz &&
24 #end if
25 #end if
26
27 ## irma command
28 IRMA '${module}'
29 #if $input_type_conditional.input_type == 'single'
30 #if $input_type_conditional.fastq_input1.is_of_type('fastq.gz')
31 file1.fastq.gz
32 #else
33 '${input_type_conditional.fastq_input1}'
34 #end if
35 #elif $input_type_conditional.input_type == 'paired_collection'
36 #if $input_type_conditional.fastq_input.forward.is_of_type('fastq.gz')
37 file1.fastq.gz
38 file2.fastq.gz
39 #else
40 '${input_type_conditional.fastq_input.forward}'
41 '${input_type_conditional.fastq_input.reverse}'
42 #end if
43 #end if
44 resultDir &&
45 ## IRMA does not write empty output files
46 ## so the following script makes sure all expected outputs exist unconditionally
47 python3 '$__tool_directory__/createMissingFiles.py' &&
48 cat irma_config.sh
49 ]]></command>
50 <configfiles>
51 <configfile filename='irma_config.sh'><![CDATA[
52 SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1}
53 DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))
54 TMP=\$TMPDIR
55 #if $advanced_config.customize == 'yes':
56 #if $advanced_config.reference == 'yes':
57 SKIP_E=$advanced_config.reference.SKIP_E
58 #end if
59 #if $advanced_config.read_gathering == 'yes':
60 MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS
61 USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN
62 QUAL_THRESHOLD=$advanced_config.read_gathering.QUAL_THRESHOLD
63 MIN_LEN=$advanced_config.read_gathering.MIN_LEN
64 INCL_CHIM=$advanced_config.read_gathering.INCL_CHIM
65 ADAPTER=$advanced_config.read_gathering.ADAPTER
66 ENFORCE_CLIPPED_LENGTH=$advanced_config.read_gathering.ENFORCE_CLIPPED_LENGTH
67 MERGE_SECONDARY=$advanced_config.read_gathering.MERGE_SECONDARY
68 RESIDUAL_ASSEMBLY_FACTOR=$advanced_config.read_gathering.RESIDUAL_ASSEMBLY_FACTOR
69 #end if
70 #if $advanced_config.match_step == 'yes':
71 MIN_RP=$advanced_config.match_step.MIN_RP
72 MIN_RC=$advanced_config.match_step.MIN_RC
73 MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH
74 #end if
75 #if $advanced_config.sort_step == 'yes':
76 SORT_PROG=$advanced_config.sort_step.SORT_PROG
77 #end if
78 #if $advanced_config.align_step == 'yes':
79 ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG
80 DEL_TYPE=$advanced_config.align_step.DEL_TYPE
81 #end if
82 #if $advanced_config.assembly == 'yes':
83 MAX_ITER_ASSEM=$advanced_config.assembly.MAX_ITER_ASSEM
84 NO_MERGE=$advanced_config.assembly.NO_MERGE
85 INS_T=$advanced_config.assembly.INS_T
86 DEL_T=$advanced_config.assembly.DEL_T
87 INS_T_DEPTH=$advanced_config.assembly.INS_T_DEPTH
88 DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH
89 SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS
90 MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG
91 SSW_M=$advanced_config.assembly.SSW_M
92 SSW_X=$advanced_config.assembly.SSW_X
93 SSW_O=$advanced_config.assembly.SSW_O
94 SSW_E=$advanced_config.assembly.SSW_E
95 ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED
96 #end if
97 #if $advanced_config.variant_calling == 'yes':
98 AUTO_F=$advanced_config.variant_calling.AUTO_F
99 MIN_FI=$advanced_config.variant_calling.MIN_FI
100 MIN_FD=$advanced_config.variant_calling.MIN_FD
101 MIN_F=$advanced_config.variant_calling.MIN_F
102 MIN_C=$advanced_config.variant_calling.MIN_C
103 MIN_AQ=$advanced_config.variant_calling.MIN_AQ
104 MIN_TCC=$advanced_config.variant_calling.MIN_TCC
105 MIN_CONF=$advanced_config.variant_calling.MIN_CONF
106 SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
107 #end if
108 #end if]]></configfile>
109 </configfiles>
110 <inputs>
111 <conditional name="input_type_conditional">
112 <param name="input_type" type="select" label="Input Type">
113 <option value="single" selected="true">Single Dataset</option>
114 <option value="paired_collection">Paired Collection</option>
115 </param>
116 <when value="single">
117 <param name="fastq_input1" type="data" format="fastq,fastq.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
118 </when>
119 <when value="paired_collection">
120 <param name="fastq_input" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
121 </when>
122 </conditional>
123 <param name="module" type="select" label="Select analysis module">
124 <option value="FLU" selected="true">FLU</option>
125 <option value="FLU-utr">FLU-utr</option>
126 <option value="FLU-pacbio">FLU-pacbio</option>
127 </param>
128 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs">
129 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option>
130 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option>
131 </param>
132 <conditional name="advanced_config">
133 <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in IRMA's default configuration file.">
134 <option value="no">No, use defaults for advanced settings</option>
135 <option value="yes">Yes</option>
136 </param>
137 <when value="no" />
138 <when value="yes">
139 <conditional name="reference">
140 <param name="customize" type="select" label="Customize Reference Settings" help="Choosing Yes here, lets you overwrite reference settings.">
141 <option value="no">No, use defaults for reference settings</option>
142 <option value="yes">Yes</option>
143 </param>
144 <when value="no" />
145 <when value="yes">
146 <param name="SKIP_E" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Skip reference elongation" />
147 </when>
148 </conditional>
149
150 <conditional name="read_gathering">
151 <param name="customize" type="select" label="Customize settings to read gathering" help="Choosing Yes here, lets you overwrite read gathering settings.">
152 <option value="no">No, use defaults for read gathering settings</option>
153 <option value="yes">Yes</option>
154 </param>
155 <when value="no" />
156 <when value="yes">
157 <param name="MAX_ROUNDS" type="integer" min="1" max="20" value="5" label="Maximal rounds of read gathering"/>
158 <param name="USE_MEDIAN" type="select" label="Use median or average for read gathering">
159 <option value="0">Average</option>
160 <option value="1" selected="true">Median</option>
161 </param>
162 <param name="QUAL_THRESHOLD" type="integer" min="0" value="30" label="Minimum read statistic to keep (Phred)"/>
163 <param name="MIN_LEN" type="integer" min="0" max="1000" value="125" label="Minimum read length to keep (bp)" />
164 <param name="INCL_CHIM" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Include chimera? Transposase adapter - clips 5' of the adapter on the forward strand and 3' on the reverse strand. applicable to NextTera pair-end reads" />
165 <param name="ADAPTER" type="text" value="AGATGTGTATAAGAGACAG" label="Adapter sequence">
166 <validator type="regex">[CAGT]+</validator>
167 </param>
168 <param name="ENFORCE_CLIPPED_LENGTH" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Reads are filtered for minimum length post adapter trimming" />
169
170 <param name="MERGE_SECONDARY" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Merge secondary data after the first round to the unmatched pool. Useful if co-infections are not expected." />
171
172 <param name="RESIDUAL_ASSEMBLY_FACTOR" type="integer" min="0" max="100" value="0" label="The ratio of match read patterns to altmatch is measured, and if its less than factor, residual assembly is performed. Set 0 for off."/>
173 </when>
174 </conditional>
175 <conditional name="match_step">
176 <param name="customize" type="select" label="Customize settings regarding the match step" help="Choosing Yes here, lets you overwrite match step settings.">
177 <option value="no">No, use defaults for match step settings</option>
178 <option value="yes">Yes</option>
179 </param>
180 <when value="no" />
181 <when value="yes">
182 <param name="MIN_RP" type="integer" min="0" value="15" label="Minimum read pattern count to continue"/>
183 <param name="MIN_RC" type="integer" min="0" value="15" label="Minimum read count to continue"/>
184 <param name="MIN_BLAT_MATCH" type="integer" min="0" value="0" label="Minimum read pattern count to continue"/>
185 </when>
186 </conditional>
187 <conditional name="sort_step">
188 <param name="customize" type="select" label="Customize settings regarding the sort step" help="Choosing Yes here, lets you overwrite sort step settings.">
189 <option value="no">No, use defaults for sort step settings</option>
190 <option value="yes">Yes</option>
191 </param>
192 <when value="no" />
193 <when value="yes">
194 <param name="SORT_PROG" type="select" label="Select program used for sorting">
195 <option value="LABEL">LABEL</option>
196 <option value="BLAT" selected="true">BLAT</option>
197 </param>
198 </when>
199 </conditional>
200 <conditional name="align_step">
201 <param name="customize" type="select" label="Customize settings regarding the alignment step" help="Choosing Yes here, lets you overwrite align step settings.">
202 <option value="no">No, use defaults for align step settings</option>
203 <option value="yes">Yes</option>
204 </param>
205 <when value="no" />
206 <when value="yes">
207 <param name="ALIGN_PROG" type="select" label="Select program used for alignment">
208 <option value="BLAT">BLAT</option>
209 <option value="SAM" selected="true">SAM</option>
210 </param>
211 <param name="DEL_TYPE" type="select" label="How to handle deletions in rough alignment">
212 <option value="" selected="true">Default</option>
213 <option value="NNN">NNN</option>
214 <option value="REF">REF</option>
215 <option value="DEL" >DEL</option>
216 </param>
217 </when>
218 </conditional>
219 <conditional name="assembly">
220 <param name="customize" type="select" label="Customize settings regarding the assembly" help="Choosing Yes here, lets you overwrite assembly settings.">
221 <option value="no">No, use defaults for assembly settings</option>
222 <option value="yes">Yes</option>
223 </param>
224 <when value="no" />
225 <when value="yes">
226 <param name="MAX_ITER_ASSEM" type="integer" min="1" value="5" label="Maximal assembly iteration"/>
227 <!-- true and false values are inverted for the next param because we're asking the opposite question of what we need to configure -->
228 <param name="NO_MERGE" type="boolean" falsevalue="1" truevalue="0" checked="true" label="Merge read pairs?" help="Merging read pairs after final assembly provides error detection and correction." />
229 <param name="INS_T" type="float" min="0" max="1" value="0.25" label="The minimum frequency threshold for insertion refinement"/>
230 <param name="DEL_T" type="float" min="0" max="1" value="0.6" label="The minimum frequency threshold for deletion refinement"/>
231 <param name="INS_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for insertion refinement"/>
232 <param name="DEL_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for deletion refinement"/>
233 <param name="SILENCE_COMPLEX_INDELS" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Silences reads with complex indels (having 4 indels with at least one greater than 9)" />
234 <param name="MIN_AMBIG" type="float" min="0" max="1" value="0.25" label="The minimum called SNV frequency for mixed base in amended consensus folder"/>
235 <param name="SSW_M" type="integer" min="1" value="2" label="The smith-waterman match score"/>
236 <param name="SSW_X" type="integer" min="1" value="5" label="The smith-waterman mismatch penalty"/>
237 <param name="SSW_O" type="integer" min="1" value="10" label="The smith-waterman gap open penalty"/>
238 <param name="SSW_E" type="integer" min="1" value="1" label="The smith-waterman gap extension penalty"/>
239 <param name="ALIGN_AMENDED" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Do global alignment of the amended consensus to the HMM profile" />
240 </when>
241 </conditional>
242 <conditional name="variant_calling">
243 <param name="customize" type="select" label="Customize settings regarding the variant calling" help="Choosing Yes here, lets you overwrite variant calling settings.">
244 <option value="no">No, use defaults for variant calling settings</option>
245 <option value="yes">Yes</option>
246 </param>
247 <when value="no" />
248 <when value="yes">
249 <param name="AUTO_F" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Automatically adjust frequency threshold" />
250 <param name="MIN_FI" type="float" min="0" max="1" value="0.005" label="The minimum insertion variant frequency"/>
251 <param name="MIN_FD" type="float" min="0" max="1" value="0.005" label="The minimum deletion variant frequency"/>
252 <param name="MIN_F" type="float" min="0" max="1" value="0.008" label="The minimum frequency for single nucleotide variants"/>
253 <param name="MIN_C" type="integer" min="1" value="2" label="The minimum count for variants"/>
254 <param name="MIN_AQ" type="integer" min="1" value="24" label="The minimum average variant quality (does not apply to deletions)"/>
255 <param name="MIN_TCC" type="integer" min="1" value="100" label="The minimum non-ambiguous column coverage"/>
256 <param name="MIN_CONF" type="float" min="0" max="1" value="0.80" label="The minimum confidence"/>
257 <param name="SIG_LEVEL" type="select" label="The significance test level for variant calling">
258 <option value="0.999" selected="true">99.9%</option>
259 <option value="0.99" >99%</option>
260 <option value="0.95" >95%</option>
261 <option value="0.90" >90%</option>
262 </param>
263 </when>
264 </conditional>
265 </when>
266 </conditional>
267 </inputs>
268 <outputs>
269 <collection name="consensus_collection" type="list" label="Fasta Consensus Sequences">
270 <data name="PB1" format="fasta" from_work_dir="resultDir/A_PB1.fasta" label="PB1"/>
271 <data name="PB2" format="fasta" from_work_dir="resultDir/A_PB2.fasta" label="PB2"/>
272 <data name="PA" format="fasta" from_work_dir="resultDir/A_PA.fasta" label="PA"/>
273 <data name="HA" format="fasta" from_work_dir="resultDir/A_HA.fasta" label="HA"/>
274 <data name="NP" format="fasta" from_work_dir="resultDir/A_NP.fasta" label="NP"/>
275 <data name="NA" format="fasta" from_work_dir="resultDir/A_NA.fasta" label="NA"/>
276 <data name="MP" format="fasta" from_work_dir="resultDir/A_MP.fasta" label="MP"/>
277 <data name="NS" format="fasta" from_work_dir="resultDir/A_NS.fasta" label="NS"/>
278 </collection>
279 <!-- optional outputs-->
280 <collection name="bam_collection" type="list" label="Alignment files (bam)">
281 <filter>optional_outputs and 'bam' in optional_outputs</filter>
282 <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/>
283 <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
284 <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/>
285 <data name="HA" format="bam" from_work_dir="resultDir/A_HA.bam" label="HA"/>
286 <data name="NP" format="bam" from_work_dir="resultDir/A_NP.bam" label="NP"/>
287 <data name="NA" format="bam" from_work_dir="resultDir/A_NA.bam" label="NA"/>
288 <data name="MP" format="bam" from_work_dir="resultDir/A_MP.bam" label="MP"/>
289 <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/>
290 </collection>
291 <collection name="vcf_collection" type="list" label="Variant calling files (VCF)">
292 <filter>optional_outputs and 'vcf' in optional_outputs</filter>
293 <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
294 <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
295 <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/>
296 <data name="HA" format="vcf" from_work_dir="resultDir/A_HA.vcf" label="HA"/>
297 <data name="NP" format="vcf" from_work_dir="resultDir/A_NP.vcf" label="NP"/>
298 <data name="NA" format="vcf" from_work_dir="resultDir/A_NA.vcf" label="NA"/>
299 <data name="MP" format="vcf" from_work_dir="resultDir/A_MP.vcf" label="MP"/>
300 <data name="NS" format="vcf" from_work_dir="resultDir/A_NS.vcf" label="NS"/>
301 </collection>
302 </outputs>
303 <tests>
304 <test expect_num_outputs="27">
305 <conditional name="input_type_conditional">
306 <param name="fastq_input1" value="test_reads.fq" />
307 <param name="input_type" value="single" />
308 </conditional>
309 <conditional name="advanced_config">
310 <param name="customize" value="no" />
311 </conditional>
312 <param name="module" value="FLU-utr" />
313 <param name="optional_outputs" value="vcf,bam"/>
314 <output_collection name="consensus_collection" type="list">
315 <element name="HA">
316 <assert_contents>
317 <has_n_lines n="2"/>
318 </assert_contents>
319 </element>
320 </output_collection>
321 </test>
322 <test expect_num_outputs="18">
323 <param name="module" value="FLU"/>
324 <param name="optional_outputs" value="bam"/>
325 <conditional name="input_type_conditional">
326 <param name="input_type" value="paired_collection"/>
327 <param name="fastq_input">
328 <collection type="paired">
329 <element name="forward" value="test_reads.fq" />
330 <element name="reverse" value="test_reads_copy.fq" />
331 </collection>
332 </param>
333 </conditional>
334 <output_collection name="consensus_collection" type="list" count="8">
335 <element name="HA">
336 <assert_contents>
337 <has_n_lines n="2"/>
338 </assert_contents>
339 </element>
340 </output_collection>
341 <output_collection name="bam_collection" type="list" count="8" />
342 </test>
343 <test expect_num_outputs="9">
344 <param name="module" value="FLU-utr"/>
345 <conditional name="input_type_conditional">
346 <param name="input_type" value="paired_collection"/>
347 <param name="fastq_input">
348 <collection type="paired">
349 <element name="forward" value="test_reads.fq" />
350 <element name="reverse" value="test_reads_copy.fq" />
351 </collection>
352 </param>
353 </conditional>
354 <conditional name="advanced_config">
355 <param name="customize" value="yes"/>
356 <conditional name="reference">
357 <param name="customize" value="yes"/>
358 <param name="SKIP_E" value="0"/>
359 </conditional>
360 <conditional name="read_gathering">
361 <param name="customize" value="yes"/>
362 <param name="MAX_ROUNDS" value="1"/>
363 </conditional>
364 </conditional>
365 <output_collection name="consensus_collection" type="list" count="8">
366 <element name="HA">
367 <assert_contents>
368 <has_n_lines n="2"/>
369 </assert_contents>
370 </element>
371 </output_collection>
372 </test>
373 <test expect_num_outputs="27">
374 <param name="module" value="FLU"/>
375 <param name="optional_outputs" value="bam,vcf"/>
376 <conditional name="input_type_conditional">
377 <param name="input_type" value="paired_collection"/>
378 <param name="fastq_input">
379 <collection type="paired">
380 <element name="forward" value="test_reads.fq" />
381 <element name="reverse" value="test_reads_copy.fq" />
382 </collection>
383 </param>
384 </conditional>
385 <conditional name="advanced_config">
386 <param name="customize" value="yes"/>
387 <conditional name="reference">
388 <param name="customize" value="yes"/>
389 <param name="SKIP_E" value="true"/>
390 </conditional>
391 <conditional name="read_gathering">
392 <param name="customize" value="yes"/>
393 <param name="MAX_ROUNDS" value="3"/>
394 <param name="USE_MEDIAN" value="1"/>
395 <param name="QUAL_THRESHOLD" value="30"/>
396 <param name="MIN_LEN" value="125"/>
397 <param name="INCL_CHIM" value="false"/>
398 <param name="ADAPTER" value="AGATGTGTATAAGAGACAG"/>
399 <param name="ENFORCE_CLIPPED_LENGTH" value="true"/>
400 <param name="MERGE_SECONDARY" value="false"/>
401 <param name="RESIDUAL_ASSEMBLY_FACTOR" value="0"/>
402 </conditional>
403 <conditional name="match_step">
404 <param name="customize" value="yes"/>
405 <param name="MIN_RP" value="15"/>
406 <param name="MIN_RC" value="15"/>
407 <param name="MIN_BLAT_MATCH" value="0"/>
408 </conditional>
409 <conditional name="sort_step">
410 <param name="customize" value="yes"/>
411 <param name="SORT_PROG" value="LABEL"/>
412 </conditional>
413 <conditional name="align_step">
414 <param name="customize" value="yes"/>
415 <param name="ALIGN_PROG" value="SAM"/>
416 <param name="DEL_TYPE" value=""/>
417 </conditional>
418 <conditional name="assembly">
419 <param name="customize" value="yes"/>
420 <param name="MAX_ITER_ASSEM" value="5"/>
421 <param name="NO_MERGE" value="false"/>
422 <param name="INS_T" value="0.25"/>
423 <param name="DEL_T" value="0.6"/>
424 <param name="INS_T_DEPTH" value="1"/>
425 <param name="DEL_T_DEPTH" value="1"/>
426 <param name="SILENCE_COMPLEX_INDELS" value="true"/>
427 <param name="MIN_AMBIG" value="0.25"/>
428 <param name="SSW_M" value="2"/>
429 <param name="SSW_X" value="5"/>
430 <param name="SSW_O" value="10"/>
431 <param name="SSW_E" value="1"/>
432 <param name="ALIGN_AMENDED" value="false"/>
433 </conditional>
434 <conditional name="variant_calling">
435 <param name="customize" value="yes"/>
436 <param name="AUTO_F" value="true"/>
437 <param name="MIN_FI" value="0.005"/>
438 <param name="MIN_FD" value="0.005"/>
439 <param name="MIN_F" value="0.008"/>
440 <param name="MIN_C" value="2"/>
441 <param name="MIN_AQ" value="24"/>
442 <param name="MIN_TCC" value="100"/>
443 <param name="MIN_CONF" value="0.80"/>
444 <param name="SIG_LEVEL" value="0.999"/>
445 </conditional>
446 </conditional>
447 <output_collection name="consensus_collection" type="list" count="8">
448 <element name="HA">
449 <assert_contents>
450 <has_n_lines n="2"/>
451 </assert_contents>
452 </element>
453 </output_collection>
454 <output_collection name="bam_collection" type="list" count="8" />
455 <output_collection name="vcf_collection" type="list" count="8" />
456 </test>
457 </tests>
458 <help><![CDATA[
459 .. class:: infomark
460
461 **What it does**
462
463 IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses.
464 These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.
465 IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this galaxy wrapper currently only supports influenza modules.
466
467 **Inputs**
468
469 Specify the module and provide your read data.
470
471 **Outputs**
472
473 The default output of the tool is a collection of consensus sequences in FASTA format.
474
475 Optionally, collections of read mapping and variant calling results can be produced as additional outputs.
476
477 **Settings**
478
479 IRMA provides carefully chosen default settings for its different analysis modes.
480 Advanced(!) users have the option to override these through the advanced config section.
481
482 .. class:: Warning mark
483
484 By enabling any section of the advanced configuration options you will override the default settings for *all* parameters in that section, and the default values of a section may not be IRMA's defaults for the selected module, but reflect IRMA's global defaults.
485
486 https://wonder.cdc.gov/amd/flu/irma/configuration.html provides more information about configuration parameters.
487 ]]></help>
488 <citations>
489 <citation type="doi">10.1186/s12864-016-3030-6</citation>
490 </citations>
491 </tool>