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comparison freebayes.xml @ 31:57def2d7c093 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
author iuc
date Sat, 27 Nov 2021 09:38:13 +0000
parents ef2c525bd8cd
children 8a7a42541080
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30:ef2c525bd8cd 31:57def2d7c093
1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@"> 1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
2 <description>bayesian genetic variant detector</description> 2 <description>bayesian genetic variant detector</description>
3 <xrefs>
4 <xref type="bio.tools">freebayes</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 </macros> 8 </macros>
6 <expand macro="requirements"> 9 <expand macro="requirements">
7 <requirement type="package" version="4.1.3">gawk</requirement> 10 <requirement type="package" version="4.1.3">gawk</requirement>
170 ## REALIGNMENT 173 ## REALIGNMENT
171 ${options_type.O} 174 ${options_type.O}
172 175
173 ##INPUT FILTERS 176 ##INPUT FILTERS
174 #if str( $options_type.input_filters.input_filters_selector ) == "set": 177 #if str( $options_type.input_filters.input_filters_selector ) == "set":
178 $standard_filters
175 ${options_type.input_filters.use_duplicate_reads} 179 ${options_type.input_filters.use_duplicate_reads}
176 -m ${options_type.input_filters.m} 180 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
177 -q ${options_type.input_filters.q} 181 --min-base-quality ${options_type.input_filters.min_base_quality}
178 -R ${options_type.input_filters.R} 182 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
179 -Y ${options_type.input_filters.Y} 183 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
180 -e ${options_type.input_filters.e}
181 -F ${options_type.input_filters.F}
182 -C ${options_type.input_filters.C}
183 -G ${options_type.input_filters.G}
184
185 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set": 184 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
186 -Q ${options_type.input_filters.mismatch_filters.Q} 185 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
187 #if str($options_type.input_filters.mismatch_filters.U) 186 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
188 -U ${options_type.input_filters.mismatch_filters.U} 187 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
189 #end if 188 #end if
190 -z ${options_type.input_filters.mismatch_filters.z} 189 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
191
192 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit} 190 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
193 #end if 191 #end if
194 192 --read-indel-limit ${options_type.input_filters.read_indel_limit}
193 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
195 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum} 194 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
195 --min-alternate-count ${options_type.input_filters.min_alternate_count}
196 --min-alternate-total ${options_type.input_filters.min_alternate_total}
196 #end if 197 #end if
197 198
198 ## POPULATION AND MAPPABILITY PRIORS 199 ## POPULATION AND MAPPABILITY PRIORS
199 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set": 200 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
200 ${options_type.population_mappability_priors.k} 201 ${options_type.population_mappability_priors.k}
466 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false" 467 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
467 label="Turn off left-alignment of indels" /> 468 label="Turn off left-alignment of indels" />
468 469
469 <!-- input filters --> 470 <!-- input filters -->
470 <conditional name="input_filters"> 471 <conditional name="input_filters">
471 <param name="input_filters_selector" type="select" label="Input filters" 472 <param name="input_filters_selector" type="select" label="Input filters">
472 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options">
473 <option value="do_not_set" selected="true">No input filters (default)</option> 473 <option value="do_not_set" selected="true">No input filters (default)</option>
474 <option value="set">Set input filters</option> 474 <option value="set">Set input filters</option>
475 </param> 475 </param>
476 <when value="set"> 476 <when value="set">
477 <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false" 477 <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
478 label="Use stringent input base and mapping quality filters"
479 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
480 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
478 label="Include duplicate-marked alignments in the analysis" /> 481 label="Include duplicate-marked alignments in the analysis" />
479 <param name="m" argument="--min-mapping-quality" type="integer" value="1" 482 <param argument="--min-mapping-quality" type="integer" value="1"
480 label="Exclude alignments from analysis if they have a mapping quality less than" /> 483 label="Exclude alignments from analysis if they have a mapping quality less than" />
481 <param name="q" argument="--min-base-quality" type="integer" value="0" 484 <param argument="--min-base-quality" type="integer" value="0"
482 label="Exclude alleles from analysis if their supporting base quality less than" /> 485 label="Exclude alleles from analysis if their supporting base quality less than" />
483 <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0" 486 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
484 label="Consider any allele in which the sum of qualities of supporting observations is at least" /> 487 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
485 <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0" 488 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
486 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" /> 489 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
487 <conditional name="mismatch_filters"> 490 <conditional name="mismatch_filters">
488 <param name="mismatch_filters_selector" type="select" label="Mismatch filters" 491 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
489 help="Sets -Q, -U, -z, and &#36; options"> 492 help="Sets -Q, -U, -z, and &#36; options">
490 <option value="do_not_set" selected="true">No mismatch filters (default)</option> 493 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
491 <option value="set">Set mismatch filters</option> 494 <option value="set">Set mismatch filters</option>
492 </param> 495 </param>
493 <when value="set"> 496 <when value="set">
494 <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10" 497 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
495 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" /> 498 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
496 <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true" 499 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
497 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)" 500 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
498 help="default=~unbounded" /> 501 help="default=~unbounded" />
499 <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0" 502 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
500 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" /> 503 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
501 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000" 504 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
502 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)" 505 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
503 help="default=~unbounded" /> 506 help="default=~unbounded" />
504 </when> 507 </when>
505 <when value="do_not_set" /> 508 <when value="do_not_set" />
506 </conditional> 509 </conditional>
507 <param name="e" argument="--read-indel-limit" type="integer" value="1000" 510 <param argument="--read-indel-limit" type="integer" value="1000"
508 label="Exclude reads with more than this number of separate gaps" 511 label="Exclude reads with more than this number of separate gaps"
509 help="default=~unbounded" /> 512 help="default=~unbounded" />
510 <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false" 513 <param argument="--min-alternate-fraction" type="float" value="0.05"
511 label="Use stringent input base and mapping quality filters"
512 help="Equivalent to -m 30 -q 20 -R 0 -S 0" />
513 <param name="F" argument="--min-alternate-fraction" type="float" value="0.05"
514 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" /> 514 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
515 <param name="C" argument="--min-alternate-count" type="integer" value="2" 515 <param argument="--min-alternate-qsum" type="integer" value="0"
516 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
517 <param argument="--min-alternate-count" type="integer" value="2"
516 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" /> 518 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
517 <param name="min_alternate_qsum" argument="--min-alternate-qsum" type="integer" value="0" 519 <param argument="--min-alternate-total" type="integer" value="1"
518 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
519 <param name="G" argument="--min-alternate-total" type="integer" value="1"
520 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" /> 520 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
521 </when> 521 </when>
522 <when value="do_not_set" /> 522 <when value="do_not_set" />
523 </conditional> 523 </conditional>
524 524