| Previous changeset 20:8fb829f953d6 (2015-07-21) Next changeset 22:99684adf84de (2015-10-09) |
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Commit message:
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d |
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modified:
freebayes.xml leftalign.xml |
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| diff -r 8fb829f953d6 -r 978760187fe2 freebayes.xml --- a/freebayes.xml Tue Jul 21 15:29:21 2015 -0400 +++ b/freebayes.xml Fri Oct 09 15:47:24 2015 -0400 |
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| @@ -351,7 +351,7 @@ <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 " /> <when value="set"> <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" /> - <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 " /> + <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 " /> </when> <when value="do_not_set"> <!-- do nothing --> @@ -454,7 +454,7 @@ <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" /> <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." /> <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" /> - <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" /> + <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" /> <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" /> <conditional name="genotype_variant_threshold"> <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" /> |
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| diff -r 8fb829f953d6 -r 978760187fe2 leftalign.xml --- a/leftalign.xml Tue Jul 21 15:29:21 2015 -0400 +++ b/leftalign.xml Fri Oct 09 15:47:24 2015 -0400 |
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| @@ -46,7 +46,7 @@ <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> - <param name="iterations" type="integer" size="3" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" /> + <param name="iterations" type="integer" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" /> </inputs> <outputs> <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" /> |