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planemo upload for repository https://github.com/aaronKol/tools-iuc/tree/main/tools/irma commit 308791d86112ad5ecfca99789841a9520e9bcb34
author iuc
date Wed, 29 Jan 2025 08:19:15 +0000
parents 69ce61289a2a
children
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2:69ce61289a2a 3:205a59cb55f1
1 <tool id="irma" name="IRMA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> 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> 2 <description>Construct robust assemblies of highly variable RNA viruses</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.2.0</token> 4 <token name="@TOOL_VERSION@">1.2.0</token>
5 <token name="@VERSION_SUFFIX@">2</token> 5 <token name="@VERSION_SUFFIX@">3</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">irma-virus</xref> 8 <xref type="bio.tools">irma-virus</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
42 #end if 42 #end if
43 #end if 43 #end if
44 resultDir && 44 resultDir &&
45 ## IRMA does not write empty output files 45 ## IRMA does not write empty output files
46 ## so the following script makes sure all expected outputs exist unconditionally 46 ## so the following script makes sure all expected outputs exist unconditionally
47 python3 '$__tool_directory__/createMissingFiles.py' && 47 python3 '$__tool_directory__/createMissingFiles.py'
48 cat irma_config.sh
49 ]]></command> 48 ]]></command>
50 <configfiles> 49 <configfiles>
51 <configfile filename='irma_config.sh'><![CDATA[ 50 <configfile filename='irma_config.sh'><![CDATA[
52 SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1} 51 SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1}
53 DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1))) 52 DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))
54 TMP=\$TMPDIR 53 TMP=\$TMPDIR
55 ASSEM_PROG="MINIMAP2" 54 ASSEM_PROG="MINIMAP2"
55 GRID_ON=0
56 SKIP_E=$SKIP_E
57 SORT_PROG="BLAT" ## LABEL is not working in galaxy docker.
56 #if $advanced_config.customize == 'yes': 58 #if $advanced_config.customize == 'yes':
57 #if $advanced_config.reference == 'yes':
58 SKIP_E=$advanced_config.reference.SKIP_E
59 #end if
60 #if $advanced_config.read_gathering == 'yes': 59 #if $advanced_config.read_gathering == 'yes':
61 MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS 60 MAX_ROUNDS=$advanced_config.read_gathering.MAX_ROUNDS
62 USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN 61 USE_MEDIAN=$advanced_config.read_gathering.USE_MEDIAN
63 QUAL_THRESHOLD=$advanced_config.read_gathering.QUAL_THRESHOLD 62 QUAL_THRESHOLD=$advanced_config.read_gathering.QUAL_THRESHOLD
64 MIN_LEN=$advanced_config.read_gathering.MIN_LEN 63 MIN_LEN=$advanced_config.read_gathering.MIN_LEN
71 #if $advanced_config.match_step == 'yes': 70 #if $advanced_config.match_step == 'yes':
72 MIN_RP=$advanced_config.match_step.MIN_RP 71 MIN_RP=$advanced_config.match_step.MIN_RP
73 MIN_RC=$advanced_config.match_step.MIN_RC 72 MIN_RC=$advanced_config.match_step.MIN_RC
74 MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH 73 MIN_BLAT_MATCH=$advanced_config.match_step.MIN_BLAT_MATCH
75 #end if 74 #end if
76 #if $advanced_config.sort_step == 'yes':
77 SORT_PROG=$advanced_config.sort_step.SORT_PROG
78 #end if
79 #if $advanced_config.align_step == 'yes': 75 #if $advanced_config.align_step == 'yes':
80 ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG 76 ALIGN_PROG=$advanced_config.align_step.ALIGN_PROG
81 DEL_TYPE=$advanced_config.align_step.DEL_TYPE 77 DEL_TYPE=$advanced_config.align_step.DEL_TYPE
82 #end if 78 #end if
83 #if $advanced_config.assembly == 'yes': 79 #if $advanced_config.assembly == 'yes':
87 DEL_T=$advanced_config.assembly.DEL_T 83 DEL_T=$advanced_config.assembly.DEL_T
88 INS_T_DEPTH=$advanced_config.assembly.INS_T_DEPTH 84 INS_T_DEPTH=$advanced_config.assembly.INS_T_DEPTH
89 DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH 85 DEL_T_DEPTH=$advanced_config.assembly.DEL_T_DEPTH
90 SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS 86 SILENCE_COMPLEX_INDELS=$advanced_config.assembly.SILENCE_COMPLEX_INDELS
91 MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG 87 MIN_AMBIG=$advanced_config.assembly.MIN_AMBIG
92 SSW_M=$advanced_config.assembly.SSW_M
93 SSW_X=$advanced_config.assembly.SSW_X
94 SSW_O=$advanced_config.assembly.SSW_O
95 SSW_E=$advanced_config.assembly.SSW_E
96 ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED 88 ALIGN_AMENDED=$advanced_config.assembly.ALIGN_AMENDED
89 MM2_A=$advanced_config.assembly.MM2_A
90 MM2_B=$advanced_config.assembly.MM2_B
91 MM2_O=$advanced_config.assembly.MM2_O
92 #if $module == "FLU-avian":
93 ## respect user choice of A,B,O,E, but configure short read presets otherwise
94 MM2_E="$advanced_config.assembly.MM2_E -x sr"
95 #else:
96 MM2_E=$advanced_config.assembly.MM2_E
97 #end if
98 #else:
99 #if $module == "FLU-avian":
100 configure short read presets for minimap2 overwriting irma module defaults where necessary
101 MM2_A=2
102 MM2_B=8
103 MM2_O="12,32"
104 MM2_E="2,1 -x sr"
105 #end if
97 #end if 106 #end if
98 #if $advanced_config.variant_calling == 'yes': 107 #if $advanced_config.variant_calling == 'yes':
99 AUTO_F=$advanced_config.variant_calling.AUTO_F 108 AUTO_F=$advanced_config.variant_calling.AUTO_F
100 MIN_FI=$advanced_config.variant_calling.MIN_FI 109 MIN_FI=$advanced_config.variant_calling.MIN_FI
101 MIN_FD=$advanced_config.variant_calling.MIN_FD 110 MIN_FD=$advanced_config.variant_calling.MIN_FD
104 MIN_AQ=$advanced_config.variant_calling.MIN_AQ 113 MIN_AQ=$advanced_config.variant_calling.MIN_AQ
105 MIN_TCC=$advanced_config.variant_calling.MIN_TCC 114 MIN_TCC=$advanced_config.variant_calling.MIN_TCC
106 MIN_CONF=$advanced_config.variant_calling.MIN_CONF 115 MIN_CONF=$advanced_config.variant_calling.MIN_CONF
107 SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL 116 SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
108 #end if 117 #end if
109 #end if]]></configfile> 118 #end if
119 ]]></configfile>
110 </configfiles> 120 </configfiles>
111 <inputs> 121 <inputs>
112 <conditional name="input_type_conditional"> 122 <conditional name="input_type_conditional">
113 <param name="input_type" type="select" label="Input Type"> 123 <param name="input_type" type="select" label="Input Type">
114 <option value="single" selected="true">Single Dataset</option> 124 <option value="single" selected="true">Single Dataset</option>
119 </when> 129 </when>
120 <when value="paired_collection"> 130 <when value="paired_collection">
121 <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"/> 131 <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"/>
122 </when> 132 </when>
123 </conditional> 133 </conditional>
124 <param name="module" type="select" label="Select analysis module"> 134 <param name="module" type="select" label="Select platform">
125 <option value="FLU" selected="true">FLU</option> 135 <option value="FLU-avian" selected="true">Illumina</option>
126 <option value="FLU-utr">FLU-utr</option> 136 <option value="FLU-minion">MinIon</option>
127 <option value="FLU-pacbio">FLU-pacbio</option> 137 <option value="FLU-pacbio">PacBio</option>
128 </param> 138 </param>
139 <param name="SKIP_E" type="boolean" falsevalue="1" truevalue="0" checked="true" label="Assemble UTRs, by elongation of reference" />
129 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs"> 140 <param name="optional_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Select additional IRMA outputs">
130 <option value="amended_consensus" selected="false">Amended consensus files: Include ambiguity codes for alleles, with second allele frequency greater 0.25</option> 141 <option value="amended_consensus" selected="false">Amended consensus files: Include ambiguity codes for alleles, with second allele frequency greater 0.25</option>
131 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option> 142 <option value="bam" selected="false">Bam: Alignment files of fastq against polished reference</option>
132 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option> 143 <option value="vcf" selected="false">Vcf: Variation calling file per segment</option>
133 <option value="run_info" selected="false">Run info: Text file with run metadata</option> 144 <option value="run_info" selected="false">Run info: Text file with run metadata</option>
137 <option value="no">No, use defaults for advanced settings</option> 148 <option value="no">No, use defaults for advanced settings</option>
138 <option value="yes">Yes</option> 149 <option value="yes">Yes</option>
139 </param> 150 </param>
140 <when value="no" /> 151 <when value="no" />
141 <when value="yes"> 152 <when value="yes">
142 <conditional name="reference">
143 <param name="customize" type="select" label="Customize Reference Settings" help="Choosing Yes here, lets you overwrite reference settings.">
144 <option value="no">No, use defaults for reference settings</option>
145 <option value="yes">Yes</option>
146 </param>
147 <when value="no" />
148 <when value="yes">
149 <param name="SKIP_E" type="boolean" falsevalue="0" truevalue="1" checked="true" label="Skip reference elongation" />
150 </when>
151 </conditional>
152
153 <conditional name="read_gathering"> 153 <conditional name="read_gathering">
154 <param name="customize" type="select" label="Customize settings to read gathering" help="Choosing Yes here, lets you overwrite read gathering settings."> 154 <param name="customize" type="select" label="Customize settings to read gathering" help="Choosing Yes here, lets you overwrite read gathering settings.">
155 <option value="no">No, use defaults for read gathering settings</option> 155 <option value="no">No, use defaults for read gathering settings</option>
156 <option value="yes">Yes</option> 156 <option value="yes">Yes</option>
157 </param> 157 </param>
185 <param name="MIN_RP" type="integer" min="0" value="15" label="Minimum read pattern count to continue"/> 185 <param name="MIN_RP" type="integer" min="0" value="15" label="Minimum read pattern count to continue"/>
186 <param name="MIN_RC" type="integer" min="0" value="15" label="Minimum read count to continue"/> 186 <param name="MIN_RC" type="integer" min="0" value="15" label="Minimum read count to continue"/>
187 <param name="MIN_BLAT_MATCH" type="integer" min="0" value="0" label="Minimum read pattern count to continue"/> 187 <param name="MIN_BLAT_MATCH" type="integer" min="0" value="0" label="Minimum read pattern count to continue"/>
188 </when> 188 </when>
189 </conditional> 189 </conditional>
190 <conditional name="sort_step">
191 <param name="customize" type="select" label="Customize settings regarding the sort step" help="Choosing Yes here, lets you overwrite sort step settings.">
192 <option value="no">No, use defaults for sort step settings</option>
193 <option value="yes">Yes</option>
194 </param>
195 <when value="no" />
196 <when value="yes">
197 <param name="SORT_PROG" type="select" label="Select program used for sorting">
198 <option value="LABEL">LABEL</option>
199 <option value="BLAT" selected="true">BLAT</option>
200 </param>
201 </when>
202 </conditional>
203 <conditional name="align_step"> 190 <conditional name="align_step">
204 <param name="customize" type="select" label="Customize settings regarding the alignment step" help="Choosing Yes here, lets you overwrite align step settings."> 191 <param name="customize" type="select" label="Customize settings regarding the alignment step" help="Choosing Yes here, lets you overwrite align step settings.">
205 <option value="no">No, use defaults for align step settings</option> 192 <option value="no">No, use defaults for align step settings</option>
206 <option value="yes">Yes</option> 193 <option value="yes">Yes</option>
207 </param> 194 </param>
233 <param name="DEL_T" type="float" min="0" max="1" value="0.6" label="The minimum frequency threshold for deletion refinement"/> 220 <param name="DEL_T" type="float" min="0" max="1" value="0.6" label="The minimum frequency threshold for deletion refinement"/>
234 <param name="INS_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for insertion refinement"/> 221 <param name="INS_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for insertion refinement"/>
235 <param name="DEL_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for deletion refinement"/> 222 <param name="DEL_T_DEPTH" type="integer" min="1" value="1" label="The minimum coverage depth for deletion refinement"/>
236 <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)" /> 223 <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)" />
237 <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"/> 224 <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"/>
238 <param name="SSW_M" type="integer" min="1" value="2" label="The smith-waterman match score"/> 225 <param name="MM2_A" type="integer" min="1" value="2" label="The minimap2 match score"/>
239 <param name="SSW_X" type="integer" min="1" value="5" label="The smith-waterman mismatch penalty"/> 226 <param name="MM2_B" type="integer" min="1" value="8" label="The minimap2 mismatch penalty"/>
240 <param name="SSW_O" type="integer" min="1" value="10" label="The smith-waterman gap open penalty"/> 227 <param name="MM2_O" type="integer" min="1" value="10" label="The minimap2 gap open penalty"/>
241 <param name="SSW_E" type="integer" min="1" value="1" label="The smith-waterman gap extension penalty"/> 228 <param name="MM2_E" type="integer" min="1" value="1" label="The minimap2 gap extension penalty"/>
242 <param name="ALIGN_AMENDED" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Do global alignment of the amended consensus to the HMM profile" /> 229 <param name="ALIGN_AMENDED" type="boolean" falsevalue="0" truevalue="1" checked="false" label="Do global alignment of the amended consensus to the HMM profile" />
243 </when> 230 </when>
244 </conditional> 231 </conditional>
245 <conditional name="variant_calling"> 232 <conditional name="variant_calling">
246 <param name="customize" type="select" label="Customize settings regarding the variant calling" help="Choosing Yes here, lets you overwrite variant calling settings."> 233 <param name="customize" type="select" label="Customize settings regarding the variant calling" help="Choosing Yes here, lets you overwrite variant calling settings.">
318 </data> 305 </data>
319 </outputs> 306 </outputs>
320 <tests> 307 <tests>
321 <test expect_num_outputs="27"> 308 <test expect_num_outputs="27">
322 <conditional name="input_type_conditional"> 309 <conditional name="input_type_conditional">
323 <param name="fastq_input1" value="test_reads.fq" /> 310 <param name="fastq_input1" value="forward.fastqsanger" />
324 <param name="input_type" value="single" /> 311 <param name="input_type" value="single" />
325 </conditional> 312 </conditional>
326 <conditional name="advanced_config"> 313 <conditional name="advanced_config">
327 <param name="customize" value="no" /> 314 <param name="customize" value="no" />
328 </conditional> 315 </conditional>
329 <param name="module" value="FLU-utr" /> 316 <param name="module" value="FLU-avian" />
317 <param name="SKIP_E" value="1" />
330 <param name="optional_outputs" value="vcf,bam"/> 318 <param name="optional_outputs" value="vcf,bam"/>
331 <output_collection name="consensus_collection" type="list"> 319 <output_collection name="consensus_collection" type="list">
332 <element name="HA"> 320 <element name="HA">
333 <assert_contents> 321 <assert_contents>
334 <has_n_lines n="2"/> 322 <has_n_lines n="2"/>
335 </assert_contents> 323 </assert_contents>
336 </element> 324 </element>
337 </output_collection> 325 </output_collection>
338 </test> 326 </test>
339 <test expect_num_outputs="18"> 327 <test expect_num_outputs="18">
340 <param name="module" value="FLU"/> 328 <param name="module" value="FLU-avian" />
329 <param name="SKIP_E" value="1" />
341 <param name="optional_outputs" value="bam"/> 330 <param name="optional_outputs" value="bam"/>
342 <conditional name="input_type_conditional"> 331 <conditional name="input_type_conditional">
343 <param name="input_type" value="paired_collection"/> 332 <param name="input_type" value="paired_collection"/>
344 <param name="fastq_input"> 333 <param name="fastq_input">
345 <collection type="paired"> 334 <collection type="paired">
346 <element name="forward" value="test_reads.fq" /> 335 <element name="forward" value="forward.fastqsanger" />
347 <element name="reverse" value="test_reads_copy.fq" /> 336 <element name="reverse" value="reverse.fastqsanger" />
348 </collection> 337 </collection>
349 </param> 338 </param>
350 </conditional> 339 </conditional>
351 <output_collection name="consensus_collection" type="list" count="8"> 340 <output_collection name="consensus_collection" type="list" count="8">
352 <element name="HA"> 341 <element name="HA">
356 </element> 345 </element>
357 </output_collection> 346 </output_collection>
358 <output_collection name="bam_collection" type="list" count="8" /> 347 <output_collection name="bam_collection" type="list" count="8" />
359 </test> 348 </test>
360 <test expect_num_outputs="9"> 349 <test expect_num_outputs="9">
361 <param name="module" value="FLU-utr"/> 350 <param name="module" value="FLU-avian" />
351 <param name="SKIP_E" value="1" />
362 <conditional name="input_type_conditional"> 352 <conditional name="input_type_conditional">
363 <param name="input_type" value="paired_collection"/> 353 <param name="input_type" value="paired_collection"/>
364 <param name="fastq_input"> 354 <param name="fastq_input">
365 <collection type="paired"> 355 <collection type="paired">
366 <element name="forward" value="test_reads.fq" /> 356 <element name="forward" value="forward.fastqsanger" />
367 <element name="reverse" value="test_reads_copy.fq" /> 357 <element name="reverse" value="reverse.fastqsanger" />
368 </collection> 358 </collection>
369 </param> 359 </param>
370 </conditional> 360 </conditional>
371 <conditional name="advanced_config"> 361 <conditional name="advanced_config">
372 <param name="customize" value="yes"/> 362 <param name="customize" value="yes"/>
373 <conditional name="reference">
374 <param name="customize" value="yes"/>
375 <param name="SKIP_E" value="0"/>
376 </conditional>
377 <conditional name="read_gathering"> 363 <conditional name="read_gathering">
378 <param name="customize" value="yes"/> 364 <param name="customize" value="yes"/>
379 <param name="MAX_ROUNDS" value="1"/> 365 <param name="MAX_ROUNDS" value="1"/>
380 </conditional> 366 </conditional>
381 </conditional> 367 </conditional>
386 </assert_contents> 372 </assert_contents>
387 </element> 373 </element>
388 </output_collection> 374 </output_collection>
389 </test> 375 </test>
390 <test expect_num_outputs="27"> 376 <test expect_num_outputs="27">
391 <param name="module" value="FLU"/> 377 <param name="module" value="FLU-pacbio" />
378 <param name="SKIP_E" value="0" />
392 <param name="optional_outputs" value="bam,vcf"/> 379 <param name="optional_outputs" value="bam,vcf"/>
393 <conditional name="input_type_conditional"> 380 <conditional name="input_type_conditional">
394 <param name="input_type" value="paired_collection"/> 381 <param name="input_type" value="paired_collection"/>
395 <param name="fastq_input"> 382 <param name="fastq_input">
396 <collection type="paired"> 383 <collection type="paired">
397 <element name="forward" value="test_reads.fq" /> 384 <element name="forward" value="forward.fastqsanger" />
398 <element name="reverse" value="test_reads_copy.fq" /> 385 <element name="reverse" value="reverse.fastqsanger" />
399 </collection> 386 </collection>
400 </param> 387 </param>
401 </conditional> 388 </conditional>
402 <conditional name="advanced_config"> 389 <conditional name="advanced_config">
403 <param name="customize" value="yes"/> 390 <param name="customize" value="yes"/>
404 <conditional name="reference">
405 <param name="customize" value="yes"/>
406 <param name="SKIP_E" value="true"/>
407 </conditional>
408 <conditional name="read_gathering"> 391 <conditional name="read_gathering">
409 <param name="customize" value="yes"/> 392 <param name="customize" value="yes"/>
410 <param name="MAX_ROUNDS" value="3"/> 393 <param name="MAX_ROUNDS" value="3"/>
411 <param name="USE_MEDIAN" value="1"/> 394 <param name="USE_MEDIAN" value="1"/>
412 <param name="QUAL_THRESHOLD" value="30"/> 395 <param name="QUAL_THRESHOLD" value="30"/>
421 <param name="customize" value="yes"/> 404 <param name="customize" value="yes"/>
422 <param name="MIN_RP" value="15"/> 405 <param name="MIN_RP" value="15"/>
423 <param name="MIN_RC" value="15"/> 406 <param name="MIN_RC" value="15"/>
424 <param name="MIN_BLAT_MATCH" value="0"/> 407 <param name="MIN_BLAT_MATCH" value="0"/>
425 </conditional> 408 </conditional>
426 <conditional name="sort_step">
427 <param name="customize" value="yes"/>
428 <param name="SORT_PROG" value="LABEL"/>
429 </conditional>
430 <conditional name="align_step"> 409 <conditional name="align_step">
431 <param name="customize" value="yes"/> 410 <param name="customize" value="yes"/>
432 <param name="ALIGN_PROG" value="SAM"/> 411 <param name="ALIGN_PROG" value="SAM"/>
433 <param name="DEL_TYPE" value=""/> 412 <param name="DEL_TYPE" value=""/>
434 </conditional> 413 </conditional>
440 <param name="DEL_T" value="0.6"/> 419 <param name="DEL_T" value="0.6"/>
441 <param name="INS_T_DEPTH" value="1"/> 420 <param name="INS_T_DEPTH" value="1"/>
442 <param name="DEL_T_DEPTH" value="1"/> 421 <param name="DEL_T_DEPTH" value="1"/>
443 <param name="SILENCE_COMPLEX_INDELS" value="true"/> 422 <param name="SILENCE_COMPLEX_INDELS" value="true"/>
444 <param name="MIN_AMBIG" value="0.25"/> 423 <param name="MIN_AMBIG" value="0.25"/>
445 <param name="SSW_M" value="2"/> 424 <param name="MM2_A" value="2"/>
446 <param name="SSW_X" value="5"/> 425 <param name="MM2_B" value="7"/>
447 <param name="SSW_O" value="10"/> 426 <param name="MM2_O" value="12"/>
448 <param name="SSW_E" value="1"/> 427 <param name="MM2_E" value="2"/>
449 <param name="ALIGN_AMENDED" value="false"/> 428 <param name="ALIGN_AMENDED" value="false"/>
450 </conditional> 429 </conditional>
451 <conditional name="variant_calling"> 430 <conditional name="variant_calling">
452 <param name="customize" value="yes"/> 431 <param name="customize" value="yes"/>
453 <param name="AUTO_F" value="true"/> 432 <param name="AUTO_F" value="true"/>
471 <output_collection name="bam_collection" type="list" count="8" /> 450 <output_collection name="bam_collection" type="list" count="8" />
472 <output_collection name="vcf_collection" type="list" count="8" /> 451 <output_collection name="vcf_collection" type="list" count="8" />
473 </test> 452 </test>
474 <test expect_num_outputs="19"> 453 <test expect_num_outputs="19">
475 <conditional name="input_type_conditional"> 454 <conditional name="input_type_conditional">
476 <param name="fastq_input1" value="test_reads.fq" /> 455 <param name="fastq_input1" value="forward.fastqsanger" />
477 <param name="input_type" value="single" /> 456 <param name="input_type" value="single" />
478 </conditional> 457 </conditional>
479 <conditional name="advanced_config"> 458 <conditional name="advanced_config">
480 <param name="customize" value="no" /> 459 <param name="customize" value="no" />
481 </conditional> 460 </conditional>
482 <param name="module" value="FLU-utr" /> 461 <param name="module" value="FLU-avian" />
462 <param name="SKIP_E" value="1" />
483 <param name="optional_outputs" value="amended_consensus,run_info"/> 463 <param name="optional_outputs" value="amended_consensus,run_info"/>
484 <output_collection name="consensus_collection" type="list"> 464 <output_collection name="consensus_collection" type="list">
485 <element name="HA"> 465 <element name="HA">
486 <assert_contents> 466 <assert_contents>
487 <has_n_lines n="2"/> 467 <has_n_lines n="2"/>
502 482
503 **What it does** 483 **What it does**
504 484
505 IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses. 485 IRMA (Iterative Refinement Meta-Assembler) can be used to obtain robust assembly, variant calling, and phasing of highly variable RNA viruses.
506 These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information. 486 These are obtained after an iterative assembly approach. Visit https://wonder.cdc.gov/amd/flu/irma/ for more information.
507 IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this galaxy wrapper currently only supports influenza modules. 487 IRMA offers modules for influenza, RSV, ebolavirus and coronavirus, but this Galaxy wrapper currently only supports influenza modules.
508 488
509 **Inputs** 489 **Inputs**
510 490
511 Specify the module and provide your read data. 491 Specify the sequencing platform and provide your read data.
512 492
513 **Outputs** 493 **Outputs**
514 494
515 The default output of the tool is a collection of consensus sequences in FASTA format. 495 The default output of the tool is a collection of majority consensus sequences in FASTA format.
516 496
517 Optionally, collections of read mapping and variant calling results can be produced as additional outputs. 497 Optionally, collections of ambiguous consensus sequences, of read mapping and variant calling results can be produced as additional outputs.
518 498
519 **Settings** 499 **Settings**
520 500
521 IRMA provides carefully chosen default settings for its different analysis modes. 501 IRMA provides carefully chosen default settings for its different analysis modes.
522 Advanced(!) users have the option to override these through the advanced config section. 502 Advanced(!) users have the option to override these through the advanced config section.
503
504 This wrapper always uses *minimap2* at the assembly step (even where the IRMA command line tool would default to SSW). For MinIon and PacBio data it uses minimap2's default long reads settings with IRMA-specific modifications of -A, -B, -O and -E parameters. For Illumina data minimap2 is run with its short-reads preset (-x sr) configuration. For all platforms, the minimap2 options -A (match score), -B (mismatch penalty), -O (gap open penalty) and -E (gap extension penalty) are user-configurable via Advanced settings -> Assembly settings.
523 505
524 .. class:: Warning mark 506 .. class:: Warning mark
525 507
526 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. 508 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.
527 509