Mercurial > repos > iuc > mykrobe_predict
diff macro.xml @ 4:a2e3ad69ee23 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
| author | iuc |
|---|---|
| date | Thu, 26 Aug 2021 20:38:36 +0000 |
| parents | e8405163fb4e |
| children |
line wrap: on
line diff
--- a/macro.xml Tue Aug 10 11:29:58 2021 +0000 +++ b/macro.xml Thu Aug 26 20:38:36 2021 +0000 @@ -1,121 +1,102 @@ -<?xml version="1.1"?> <macros> - <token name="@TOOL_VERSION@">0.10.0</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement> - </requirements> - </xml> - <token name="@select_inputs@"> - <![CDATA[ - #set $name='sample' - ]]> - </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 + <token name="@TOOL_VERSION@">0.10.0</token> + <token name="@PROFILE@">20.09</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement> + </requirements> + </xml> - #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 + <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> - #if $ploidy: - --ploidy '${ploidy}' - #end if - ]]> - </token> - - <xml name="inputs"> - <conditional name="data_type"> - <param name="type" type="select" label="Specify the read type."> - <option value="single">Single-end Data</option> - <option value="paired">Paired-end Data</option> - <option value="collection">Collection Paired-end Data</option> - </param> - <when value="single"> - <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/> - </when> - <when value="paired"> - <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/> - <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/> - </when> - <when value="collection"> - <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" /> - </when> - </conditional> - </xml> + <xml name="inputs"> + <conditional name="data_type"> + <param name="type" type="select" label="Specify the read type."> + <option value="single">Single-end Data</option> + <option value="paired">Paired-end Data</option> + <option value="collection">Collection Paired-end Data</option> + </param> + <when value="single"> + <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/> + </when> + <when value="paired"> + <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/> + <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/> + </when> + <when value="collection"> + <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" /> + </when> + </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> + <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[ - - **MyKrobe predict - Antibiotic resistance predictions** - - Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis - using Bruijn graph. - ]]> - </token> + <token name="@ATTRIBUTION@"> + <![CDATA[ + **MyKrobe predict - Antibiotic resistance predictions** + Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis + using Bruijn graph. + ]]> + </token> - <xml name="citation"> - <citations> - <citation type="doi">10.1038/ncomms10063</citation> - </citations> - </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1038/ncomms10063</citation> + </citations> + </xml> </macros>