| Previous changeset 0:d783eb846f59 (2018-01-13) Next changeset 2:0f4a5de7878a (2020-01-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449 |
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modified:
macro.xml mykrobe_genotype.xml |
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| diff -r d783eb846f59 -r 84f769706f7a macro.xml --- a/macro.xml Sat Jan 13 09:02:58 2018 -0500 +++ b/macro.xml Tue Apr 02 11:57:05 2019 -0400 |
| [ |
| @@ -2,10 +2,9 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.5.6">mykrobe</requirement> + <requirement type="package" version="0.6.1">mykrobe</requirement> </requirements> </xml> - <token name="@select_inputs@"> <![CDATA[ #set $name='sample' @@ -39,6 +38,57 @@ ]]> </token> + <token name="@shared_options@"> + <![CDATA[ + #if $kmer: + --kmer '${kmer}' + #end if + #if $expected_depth: + --expected_depth '${expected_depth}' + #end if + + $ont + + $report_all_calls + + #if $expected_error_rate: + --expected_error_rate '${expected_error_rate}' + #end if + + #if $min_variant_conf: + --min_variant_conf '${min_variant_conf}' + #end if + + #if $min_gene_conf: + --min_gene_conf '${min_gene_conf}' + #end if + + #if $min_proportion_expected_depth: + --min_proportion_expected_depth '${min_proportion_expected_depth}' + #end if + + #if $min_gene_percent_covg_threshold: + --min_gene_percent_covg_threshold '${min_gene_percent_covg_threshold}' + #end if + + $guess_sequence_method + + $ignore_minor_calls + + #if $ignore_filtered: + --ignore_filtered '${ignore_filtered}' + #end if + + #if $model: + --model '${model}' + #end if + + #if $ploidy: + --ploidy '${ploidy}' + #end if + ]]> + </token> + <xml name="inputs"> <conditional name="data_type"> <param name="type" type="select" label="Specify the read type."> @@ -59,6 +109,26 @@ </conditional> </xml> + <xml name="options"> + <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/> + <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate" help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/> + <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/> + <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/> + <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/> + <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/> + <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage" help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/> + <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/> + <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/> + <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model"> + <option value="diploid">diploid</option> + <option value="haploid">haploid</option> + </param> + <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/> + <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/> + <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/> + <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method" help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/> + </xml> + <token name="@ATTRIBUTION@"> <![CDATA[ |
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| diff -r d783eb846f59 -r 84f769706f7a mykrobe_genotype.xml --- a/mykrobe_genotype.xml Sat Jan 13 09:02:58 2018 -0500 +++ b/mykrobe_genotype.xml Tue Apr 02 11:57:05 2019 -0400 |
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| @@ -1,5 +1,4 @@ -<?xml version="1.0" encoding="utf-8"?> -<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.5.6" > +<tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.6.1" > <description>Antibiotic resistance predictions</description> <macros> <import>macro.xml</import> @@ -10,17 +9,14 @@ @select_inputs@ mykrobe genotype - '$name' - '$probe_set' + '${name}' + '${probe_set}' - #if $kmer: - --kmer $kmer + #if $filter: + --filters '${filter}' #end if - #if $expected_depth: - --expected_depth $expected_depth - #end if - + @shared_options@ -q -t "\${GALAXY_SLOTS:-1}" @@ -33,14 +29,14 @@ #else *.fasta #end if - > $json + > '$json' ]]> </command> <inputs> <expand macro="inputs" /> - <param name="probe_set" type="data" format="fasta" label="Probe Set"/> - <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/> - <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth" help=""/> + <param argument="--probe_set" type="data" format="fasta" label="Probe Set"/> + <param argument="--filter" type="data" format="txt,fasta" label="Filter Genotypes" optional="True" help="Don't include filtered genotypes"/> + <expand macro="options"/> </inputs> <outputs> <data name="json" format="json" label="JSON prediction"/> |