Mercurial > repos > iuc > bcftools_call
changeset 21:1001172b5089 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
| author | iuc |
|---|---|
| date | Tue, 16 Jul 2024 17:07:11 +0000 |
| parents | f0d44631365f |
| children | |
| files | bcftools_call.xml macros.xml |
| diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/bcftools_call.xml Thu Jan 12 15:39:40 2023 +0000 +++ b/bcftools_call.xml Tue Jul 16 17:07:11 2024 +0000 @@ -139,14 +139,14 @@ </when> <when value="alleles"> <expand macro="macro_restrictions_file" type="target" label_type="Target" /> - <param name="insert_missed" argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" /> + <param argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" /> </when> <when value="trio"> <expand macro="macro_restrict" type="target" label_type="Target" /> <expand macro="macro_novel_rate" /> </when> </conditional> - <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> + <param argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> <help> <![CDATA[ For example: --prior-freqs REF_AN,REF_AC @@ -172,7 +172,7 @@ </when> </conditional> <expand macro="macro_restrict" type="target" label_type="Target" /> - <param name="pval_threshold" argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)<FLOAT" /> + <param argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)<FLOAT" /> </when> </conditional> </section> @@ -184,23 +184,23 @@ <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option> <option value="1">1 - Treat all samples as haploid</option> </param> - <param name="ploidy_file" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> + <param argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> <expand macro="macro_restrict" /> <expand macro="macro_samples" /> </section> <section name="sec_input_output" expanded="false" title="Input/output Options"> - <param name="group_samples" argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" /> - <param name="keep_alts" argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" /> - <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample" + <param argument="--group-samples" type="boolean" truevalue="--group-samples -" falsevalue="" label="Single Sample Calling" help="Group samples by population for single-sample calling (-G - is the only option implemented so far)" /> + <param argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" /> + <param argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample" help="Currently GQ and GP fields are supported" > <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator> </param> - <param name="keep_masked_ref" argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" /> - <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites"> + <param argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" /> + <param argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites"> <option value="indels">indels</option> <option value="snps">snps</option> </param> - <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" /> + <param argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" /> <expand macro="macro_output_tags"> <option value="INFO/PV4">INFO/PV4: P-values for strand bias, baseQ bias, mapQ bias and tail</option> <option value="FORMAT/GQ">FORMAT/GQ: Phred-scaled genotype quality</option>
--- a/macros.xml Thu Jan 12 15:39:40 2023 +0000 +++ b/macros.xml Tue Jul 16 17:07:11 2024 +0000 @@ -174,7 +174,7 @@ </token> <xml name="macro_AF_file"> - <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> + <param argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> </xml> <!-- This may need to bgzip and tabix the file --> <token name="@PREPARE_AF_FILE@"> @@ -191,7 +191,7 @@ </token> <xml name="macro_estimate_AF"> - <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> + <param argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> </xml> <token name="@ESTIMATE_AF@"> #if 'estimate_AF' in $section and $section.estimate_AF: