Mercurial > repos > iuc > polypolish
comparison polypolish.xml @ 0:0c094ece2c73 draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
| author | iuc |
|---|---|
| date | Thu, 22 Sep 2022 07:50:58 +0000 |
| parents | |
| children | df205c588e6f |
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| -1:000000000000 | 0:0c094ece2c73 |
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| 1 <tool id="polypolish" name="Polypolish" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description> | |
| 3 Short-read polishing of long-read bacterial genome assemblies | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macro.xml</import> | |
| 7 </macros> | |
| 8 <expand macro='xrefs'/> | |
| 9 <expand macro="requirements" /> | |
| 10 <expand macro="version_command" /> | |
| 11 <command detect_errors="aggressive"><![CDATA[ | |
| 12 ln -s '$input.fasta_file' input_data && | |
| 13 #*====================================== | |
| 14 For single SAM | |
| 15 ======================================*# | |
| 16 #if $input.sam_data_type.sam_selector == 'single' | |
| 17 #if $input.sam_data_type.single_sam.ext == 'unsorted.bam' | |
| 18 samtools view -h $input.sam_data_type.single_sam > input_sam && | |
| 19 #elif $input.sam_data_type.single_sam.ext == 'sam' | |
| 20 ln -s $input.sam_data_type.single_sam input_sam && | |
| 21 #end if | |
| 22 polypolish input_data input_sam > '$polished_fasta' | |
| 23 #*====================================== | |
| 24 For paired SAM | |
| 25 ======================================*# | |
| 26 #elif $input.sam_data_type.sam_selector == 'paired' | |
| 27 #if $input.sam_data_type.R1_sam.ext == 'unsorted.bam' | |
| 28 samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam && | |
| 29 #elif $input.sam_data_type.R1_sam.ext == 'sam' | |
| 30 ln -s '$input.sam_data_type.R1_sam' sample_R1.sam && | |
| 31 #end if | |
| 32 #if $input.sam_data_type.R2_sam.ext == 'unsorted.bam' | |
| 33 samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam && | |
| 34 #elif $input.sam_data_type.R2_sam.ext == 'sam' | |
| 35 ln -s '$input.sam_data_type.R2_sam' sample_R2.sam && | |
| 36 #end if | |
| 37 #if $input.sam_data_type.insert_filter.filter_select == 'filter' | |
| 38 polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low' | |
| 39 --high '$input.sam_data_type.insert_filter.high' | |
| 40 --in1 sample_R1.sam | |
| 41 --in2 sample_R2.sam | |
| 42 --out1 'filtered_1.sam' | |
| 43 --out2 'filtered_2.sam' && | |
| 44 polypolish input_data 'filtered_1.sam' 'filtered_2.sam' > $polished_fasta | |
| 45 #else | |
| 46 polypolish input_data sample_R1.sam sample_R2.sam > $polished_fasta | |
| 47 #end if | |
| 48 #*====================================== | |
| 49 For multiple single-end SAM | |
| 50 ======================================*# | |
| 51 #elif $input.sam_data_type.sam_selector == 'multiple_single' | |
| 52 mkdir single_collection && | |
| 53 #for $value, $single_sam in enumerate($input.sam_data_type.single_collection): | |
| 54 #if $single_sam.ext == 'unsorted.bam' | |
| 55 samtools view -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' && | |
| 56 #elif $single_sam.ext == 'sam' | |
| 57 ln -s $single_sam 'single_collection/$(single_sam.element_identifier).$(single_sam.ext)' && | |
| 58 #end if | |
| 59 #end for | |
| 60 polypolish input_data single_collection/*.sam > '$polished_fasta' | |
| 61 #*====================================== | |
| 62 For multiple paired-end SAM | |
| 63 ======================================*# | |
| 64 #elif $input.sam_data_type.sam_selector == "multiple_paired" | |
| 65 mkdir paired_collection && | |
| 66 #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection): | |
| 67 #if $paired_sam.forward.ext == 'unsorted.bam' | |
| 68 samtools view -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && | |
| 69 #else | |
| 70 ln -s '$paired_sam.forward' 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && | |
| 71 #end if | |
| 72 #if $paired_sam.reverse.ext == 'unsorted.bam' | |
| 73 samtools view -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && | |
| 74 #else | |
| 75 ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && | |
| 76 #end if | |
| 77 #if $input.sam_data_type.insert_filter.filter_select == 'filter' | |
| 78 polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low' | |
| 79 --high '$input.sam_data_type.insert_filter.high' | |
| 80 --in1 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' | |
| 81 --in2 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' | |
| 82 --out1 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier)_filtered.sam' | |
| 83 --out2 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier)_filtered.sam' && | |
| 84 #end if | |
| 85 #end for | |
| 86 #*====================================== | |
| 87 Filtering option | |
| 88 ======================================*# | |
| 89 #if $input.sam_data_type.insert_filter.filter_select == 'filter' | |
| 90 polypolish input_data paired_collection/*_filtered.sam > '$polished_fasta' | |
| 91 #else | |
| 92 polypolish input_data paired_collection/*.sam > '$polished_fasta' | |
| 93 #end if | |
| 94 #end if | |
| 95 #*====================================== | |
| 96 For debug file output | |
| 97 ======================================*# | |
| 98 #if $options.debug == 'true' | |
| 99 --debug $debug_file | |
| 100 #end if | |
| 101 #*====================================== | |
| 102 For LOGFILE OUTPUT | |
| 103 ======================================*# | |
| 104 #if $options.keep_logfile == 'true' | |
| 105 | tee '$logfile' | |
| 106 #end if | |
| 107 ]]> | |
| 108 </command> | |
| 109 <inputs> | |
| 110 <section name="input" title="Input sequences" expanded="True"> | |
| 111 <param name="fasta_file" type="data" format="fasta" label="Select a draft genome for polishing" | |
| 112 help="Fasta sequence to be cleaned using short-reads data"/> | |
| 113 <conditional name="sam_data_type"> | |
| 114 <param name="sam_selector" type="select" label="Select aligned data to polish" help="Choose number of aligned sam/bam files. Need aligned file with all possible locations in aligner option"> | |
| 115 <option value="single">Single SAM/BAM file</option> | |
| 116 <option value="paired">Paired SAM/BAM files</option> | |
| 117 <option value="multiple_single">Multiple single SAM/BAM files</option> | |
| 118 <option value="multiple_paired">Multiple paired SAM/BAM files</option> | |
| 119 </param> | |
| 120 <when value="single"> | |
| 121 <param name="single_sam" type="data" format="sam,unsorted.bam" label="Select a SAM/BAM file" help="Specify dataset with only one SAM/BAM file"/> | |
| 122 </when> | |
| 123 <when value="paired"> | |
| 124 <param name="R1_sam" type="data" format="sam,unsorted.bam" label="Select forward SAM/BAM file" help="Specify the forward SAM/BAM files"/> | |
| 125 <param name="R2_sam" type="data" format="sam,unsorted.bam" label="Select reverse SAM/BAM file" help="Specify the reverse SAM/BAM files"/> | |
| 126 <expand macro="filter_option"/> | |
| 127 </when> | |
| 128 <when value="multiple_single"> | |
| 129 <param name="single_collection" format="sam,unsorted.bam" type="data_collection" collection_type="list" label="Single-end collection" help="Specify a list of single-end dataset"/> | |
| 130 </when> | |
| 131 <when value="multiple_paired"> | |
| 132 <param name="paired_collection" format="sam,unsorted.bam" type="data_collection" collection_type="list:paired" label="Single-end collection" help="Specify a list of single-end dataset"/> | |
| 133 <expand macro="filter_option"/> | |
| 134 </when> | |
| 135 </conditional> | |
| 136 </section> | |
| 137 <section name="options" title="Options" expanded="False"> | |
| 138 <param name="min_depth" argument="--min_depth" type="integer" min="0" value="5" label="Minimal depth" | |
| 139 help="A base must occur at least this many times in the pileup to be considered valid [default: 5]"/> | |
| 140 <param name="fraction_invalid" argument="--fraction_invalid" type="float" min="0" value="0.2" max="1" label="Minimal invalid fraction" | |
| 141 help="A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"/> | |
| 142 <param name="max_errors" argument="--max_errors" type="integer" min="0" value="10" label="Number of mismatch/indels to ignore alignments" | |
| 143 help="Ignore alignments with more than this many mismatches and indels [default: 10]"/> | |
| 144 <param name="fraction_valid" argument="--fraction_valid" type="float" min="0" value="0.5" max="1" label="Minimal valid fraction" | |
| 145 help="A base must make up at least this fraction of the read depth to be considered valid [default: 0.5"/> | |
| 146 <param name="keep_logfile" type="boolean" truevalue="true" falsevalue="false" label="Keep log file"/> | |
| 147 <param name="debug" argument="--debug" type="boolean" truevalue="true" falsevalue="false" label="Keep per base information file"/> | |
| 148 </section> | |
| 149 </inputs> | |
| 150 <outputs> | |
| 151 <data name="polished_fasta" format="fasta" label="${tool.name} on ${on_string}: polished fasta"/> | |
| 152 <data name="debug_file" format="tabular" label="${tool.name} on ${on_string}: Per base informations"> | |
| 153 <filter> options['debug'] == True </filter> | |
| 154 </data> | |
| 155 <data name="logfile" format="txt" from_work_dir="output" label="${tool.name} on ${on_string}: log report"> | |
| 156 <filter> options['keep_logfile'] == True </filter> | |
| 157 </data> | |
| 158 </outputs> | |
| 159 <tests> | |
| 160 <!-- Test_1 with default values and single SAM --> | |
| 161 <test expect_num_outputs="1"> | |
| 162 <section name="input"> | |
| 163 <param name="fasta_file" value="contigs.fa"/> | |
| 164 <conditional name="sam_data_type"> | |
| 165 <param name="sam_selector" value="single"/> | |
| 166 <param name="single_sam" value="aligned_test_file/alignement_R1.sam"/> | |
| 167 </conditional> | |
| 168 </section> | |
| 169 <output name="polished_fasta" value="polished.fasta"/> | |
| 170 </test> | |
| 171 <!-- Test_2 with default values and paired SAM --> | |
| 172 <test expect_num_outputs="2"> | |
| 173 <section name="input"> | |
| 174 <param name="fasta_file" value="contigs.fa"/> | |
| 175 <conditional name="sam_data_type"> | |
| 176 <param name="sam_selector" value="paired"/> | |
| 177 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> | |
| 178 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> | |
| 179 </conditional> | |
| 180 </section> | |
| 181 <section name="options"> | |
| 182 <param name="debug" value="true"/> | |
| 183 <param name="keep_logfile" value="false"/> | |
| 184 </section> | |
| 185 <output name="polished_fasta" value="polished.fasta"/> | |
| 186 <output name="debug_file" value="debug_file_test_2.tsv"/> | |
| 187 </test> | |
| 188 <!-- Test_3 with default values and single-end multiple SAM --> | |
| 189 <test expect_num_outputs="2"> | |
| 190 <section name="input"> | |
| 191 <param name="fasta_file" value="contigs.fa"/> | |
| 192 <conditional name="sam_data_type"> | |
| 193 <param name="sam_selector" value="multiple_single"/> | |
| 194 <param name="single_collection"> | |
| 195 <collection type="list"> | |
| 196 <element name="R1_sam" value="aligned_test_file/alignement_R1.sam" ftype="sam"/> | |
| 197 <element name="R1_bis_sam" value="aligned_test_file/alignement_R1_bis.sam" ftype="sam"/> | |
| 198 <element name="R1_ter_sam" value="aligned_test_file/alignement_R1_ter.sam" ftype="sam"/> | |
| 199 </collection> | |
| 200 </param> | |
| 201 </conditional> | |
| 202 </section> | |
| 203 <section name="options"> | |
| 204 <param name="debug" value="false"/> | |
| 205 <param name="keep_logfile" value="true"/> | |
| 206 </section> | |
| 207 <output name="polished_fasta" value="polished.fasta"/> | |
| 208 <output name="logfile" value="logfile_test_3.log" lines_diff="15"/> | |
| 209 </test> | |
| 210 <!-- Test_4 with default values and paired collection SAM --> | |
| 211 <test expect_num_outputs="1"> | |
| 212 <section name="input"> | |
| 213 <param name="fasta_file" value="contigs.fa"/> | |
| 214 <conditional name="sam_data_type"> | |
| 215 <param name="sam_selector" value="multiple_paired"/> | |
| 216 <param name="paired_collection"> | |
| 217 <collection type="list:paired"> | |
| 218 <element name="paired_1"> | |
| 219 <collection type="paired"> | |
| 220 <element name="forward" value="aligned_test_file/alignement_R1.sam" ftype="sam"/> | |
| 221 <element name="reverse" value="aligned_test_file/alignement_R2.sam" ftype="sam"/> | |
| 222 </collection> | |
| 223 </element> | |
| 224 <element name="paired_2"> | |
| 225 <collection type="paired"> | |
| 226 <element name="forward" value="aligned_test_file/alignement_R1_bis.sam" ftype="sam"/> | |
| 227 <element name="reverse" value="aligned_test_file/alignement_R2_bis.sam" ftype="sam"/> | |
| 228 </collection> | |
| 229 </element> | |
| 230 <element name="paired_3"> | |
| 231 <collection type="paired"> | |
| 232 <element name="forward" value="aligned_test_file/alignement_R1_ter.sam" ftype="sam"/> | |
| 233 <element name="reverse" value="aligned_test_file/alignement_R2_ter.sam" ftype="sam"/> | |
| 234 </collection> | |
| 235 </element> | |
| 236 </collection> | |
| 237 </param> | |
| 238 </conditional> | |
| 239 </section> | |
| 240 <output name="polished_fasta" value="polished.fasta"/> | |
| 241 </test> | |
| 242 <!-- Test_5 paired-end without filtering and whitout log file --> | |
| 243 <test expect_num_outputs="1"> | |
| 244 <section name="input"> | |
| 245 <param name="fasta_file" value="contigs.fa"/> | |
| 246 <conditional name="sam_data_type"> | |
| 247 <param name="sam_selector" value="paired"/> | |
| 248 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> | |
| 249 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> | |
| 250 </conditional> | |
| 251 </section> | |
| 252 <section name="options"> | |
| 253 <conditional name="insert_filter"> | |
| 254 <param name="filter_select" value="non_filter"/> | |
| 255 </conditional> | |
| 256 <param name="debug" value="false"/> | |
| 257 <param name="keep_logfile" value="false"/> | |
| 258 </section> | |
| 259 <output name="polished_fasta" value="polished.fasta"/> | |
| 260 </test> | |
| 261 <!-- Test_6 paired-end with filter, user defined values and whitout log file --> | |
| 262 <test expect_num_outputs="1"> | |
| 263 <section name="input"> | |
| 264 <param name="fasta_file" value="contigs.fa"/> | |
| 265 <conditional name="sam_data_type"> | |
| 266 <param name="sam_selector" value="paired"/> | |
| 267 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> | |
| 268 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> | |
| 269 <conditional name="insert_filter"> | |
| 270 <param name="filter_select" value="filter"/> | |
| 271 <param name="low" value="1"/> | |
| 272 <param name="high" value="98.7"/> | |
| 273 </conditional> | |
| 274 </conditional> | |
| 275 </section> | |
| 276 <section name="options"> | |
| 277 <param name="debug" value="false"/> | |
| 278 <param name="keep_logfile" value="false"/> | |
| 279 </section> | |
| 280 <output name="polished_fasta" value="polished.fasta"/> | |
| 281 </test> | |
| 282 <!-- Test_7 paired-end with all customized filters --> | |
| 283 <test expect_num_outputs="1"> | |
| 284 <section name="input"> | |
| 285 <param name="fasta_file" value="contigs.fa"/> | |
| 286 <conditional name="sam_data_type"> | |
| 287 <param name="sam_selector" value="paired"/> | |
| 288 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> | |
| 289 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> | |
| 290 <conditional name="insert_filter"> | |
| 291 <param name="filter_select" value="filter"/> | |
| 292 <param name="low" value="1.4"/> | |
| 293 <param name="high" value="96.6"/> | |
| 294 </conditional> | |
| 295 </conditional> | |
| 296 </section> | |
| 297 <section name="options"> | |
| 298 <param name="min_depth" value="10"/> | |
| 299 <param name="fraction_invalid" value="0.5"/> | |
| 300 <param name="max_errors" value="8"/> | |
| 301 <param name="fraction_valid" value="0.6"/> | |
| 302 <param name="debug" value="false"/> | |
| 303 <param name="keep_logfile" value="false"/> | |
| 304 </section> | |
| 305 <output name="polished_fasta" value="polished.fasta"/> | |
| 306 </test> | |
| 307 <!-- Test_8 single with bam input --> | |
| 308 <test expect_num_outputs="1"> | |
| 309 <section name="input"> | |
| 310 <param name="fasta_file" value="contigs.fa"/> | |
| 311 <conditional name="sam_data_type"> | |
| 312 <param name="sam_selector" value="single"/> | |
| 313 <param name="single_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> | |
| 314 </conditional> | |
| 315 </section> | |
| 316 <section name="options"> | |
| 317 <param name="debug" value="false"/> | |
| 318 <param name="keep_logfile" value="false"/> | |
| 319 </section> | |
| 320 <output name="polished_fasta" value="polished.fasta"/> | |
| 321 </test> | |
| 322 <!-- Test_9 paired-end with bam input --> | |
| 323 <test expect_num_outputs="1"> | |
| 324 <section name="input"> | |
| 325 <param name="fasta_file" value="contigs.fa"/> | |
| 326 <conditional name="sam_data_type"> | |
| 327 <param name="sam_selector" value="paired"/> | |
| 328 <param name="R1_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> | |
| 329 <param name="R2_sam" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/> | |
| 330 </conditional> | |
| 331 </section> | |
| 332 <section name="options"> | |
| 333 <param name="debug" value="false"/> | |
| 334 <param name="keep_logfile" value="false"/> | |
| 335 </section> | |
| 336 <output name="polished_fasta" value="polished.fasta"/> | |
| 337 </test> | |
| 338 <!-- Test_10 single collection with bam input --> | |
| 339 <test expect_num_outputs="1"> | |
| 340 <section name="input"> | |
| 341 <param name="fasta_file" value="contigs.fa"/> | |
| 342 <conditional name="sam_data_type"> | |
| 343 <param name="sam_selector" value="multiple_single"/> | |
| 344 <param name="single_collection"> | |
| 345 <collection type="list"> | |
| 346 <element name="R1_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> | |
| 347 <element name="R1_bis_sam" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/> | |
| 348 <element name="R1_ter_sam" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/> | |
| 349 </collection> | |
| 350 </param> | |
| 351 </conditional> | |
| 352 </section> | |
| 353 <section name="options"> | |
| 354 <param name="debug" value="false"/> | |
| 355 <param name="keep_logfile" value="false"/> | |
| 356 </section> | |
| 357 <output name="polished_fasta" value="polished.fasta"/> | |
| 358 </test> | |
| 359 <!-- Test_11 paired-end with bam input --> | |
| 360 <test expect_num_outputs="1"> | |
| 361 <section name="input"> | |
| 362 <param name="fasta_file" value="contigs.fa"/> | |
| 363 <conditional name="sam_data_type"> | |
| 364 <param name="sam_selector" value="multiple_paired"/> | |
| 365 <param name="paired_collection"> | |
| 366 <collection type="list:paired"> | |
| 367 <element name="paired_1"> | |
| 368 <collection type="paired"> | |
| 369 <element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> | |
| 370 <element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/> | |
| 371 </collection> | |
| 372 </element> | |
| 373 <element name="paired_2"> | |
| 374 <collection type="paired"> | |
| 375 <element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/> | |
| 376 <element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/> | |
| 377 </collection> | |
| 378 </element> | |
| 379 <element name="paired_3"> | |
| 380 <collection type="paired"> | |
| 381 <element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/> | |
| 382 <element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/> | |
| 383 </collection> | |
| 384 </element> | |
| 385 </collection> | |
| 386 </param> | |
| 387 </conditional> | |
| 388 </section> | |
| 389 <section name="options"> | |
| 390 <param name="debug" value="false"/> | |
| 391 <param name="keep_logfile" value="false"/> | |
| 392 </section> | |
| 393 <output name="polished_fasta" value="polished.fasta"/> | |
| 394 </test> | |
| 395 </tests> | |
| 396 <help><![CDATA[ | |
| 397 **What it does** | |
| 398 Polypolish is a tool for polishing genome assemblies with short reads. | |
| 399 Polypolish uses SAM/BAM files where each read has been aligned to all possible locations (not just a single best location). | |
| 400 This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. | |
| 401 | |
| 402 **Polypolish pipeline steps** | |
| 403 1. [Optional] Filter aligned reads | |
| 404 - Exclude some alignments based on their insert size | |
| 405 - This should reduce the number of excessive alignments, particularly near the edges of repeat sequences, improving Polypolish's ability to fix errors in those regions. | |
| 406 2. Clean assembly with filtered reads | |
| 407 | |
| 408 **Inputs** | |
| 409 Polypolish need SAM/BAM input format obtain from aligner with option to keep all possible location | |
| 410 Polypolish take on or more assembly as input fasta. | |
| 411 It need also raw data reads in single or paired-end SAM/BAM format. | |
| 412 You can use multiple aligned data to polish the same assembly. | |
| 413 **WARNING It can only work if multiple location information is available in sam/bam files** | |
| 414 For example using bwa mem to align raw data before use, you need : | |
| 415 1. To align each read data independantly (also for paired data) | |
| 416 2. Set the option "Output all alignments for single-ends or unpaired paired-ends" in Select analysis mode>Set input/output options | |
| 417 - This allow multiple ailgnemnt output need to use polypolish | |
| 418 | |
| 419 | |
| 420 ]]></help> | |
| 421 <expand macro="citations"/> | |
| 422 </tool> |