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comparison freebayes.xml @ 21:978760187fe2 draft

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planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d
author devteam
date Fri, 09 Oct 2015 15:47:24 -0400
parents 8fb829f953d6
children 99684adf84de
comparison
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20:8fb829f953d6 21:978760187fe2
349 349
350 <conditional name="reference_allele"> 350 <conditional name="reference_allele">
351 <param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options " /> 351 <param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options " />
352 <when value="set"> 352 <when value="set">
353 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" help="-Z --use-reference-allele; default=False" /> 353 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" help="-Z --use-reference-allele; default=False" />
354 <param name="reference_quality" type="text" size="8" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60 " /> 354 <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60 " />
355 </when> 355 </when>
356 <when value="do_not_set"> 356 <when value="do_not_set">
357 <!-- do nothing --> 357 <!-- do nothing -->
358 </when> 358 </when>
359 </conditional> 359 </conditional>
452 <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak algorithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " /> 452 <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak algorithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " />
453 <when value="set"> 453 <when value="set">
454 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" /> 454 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" />
455 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." /> 455 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
456 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" help="--genotyping-max-banddepth; default=6" /> 456 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" help="--genotyping-max-banddepth; default=6" />
457 <param name="W" type="text" size="8" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" /> 457 <param name="W" type="text" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" />
458 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" help="-N --exclude-unobserved-genotypes; default=False" /> 458 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" help="-N --exclude-unobserved-genotypes; default=False" />
459 <conditional name="genotype_variant_threshold"> 459 <conditional name="genotype_variant_threshold">
460 <param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" /> 460 <param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" />
461 <when value="do_not_set"> 461 <when value="do_not_set">
462 <!-- do nothing --> 462 <!-- do nothing -->