Mercurial > repos > iuc > mykrobe_predict

comparison macro.xml @ 4:70a3a5377e6d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
author iuc
date Thu, 26 Aug 2021 20:37:45 +0000
parents 0f2f9e53b6fa
children
comparison
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3:0f2f9e53b6fa 4:70a3a5377e6d
1 <?xml version="1.1"?>
2 <macros> 1 <macros>
3 <token name="@TOOL_VERSION@">0.10.0</token> 2 <token name="@TOOL_VERSION@">0.10.0</token>
4 <xml name="requirements"> 3 <token name="@PROFILE@">20.09</token>
5 <requirements> 4 <xml name="requirements">
6 <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement> 5 <requirements>
7 </requirements> 6 <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
8 </xml> 7 </requirements>
9 <token name="@select_inputs@"> 8 </xml>
10 <![CDATA[
11 #set $name='sample'
12 ]]>
13 </token>
14 9
15 <token name="@shared_options@"> 10 <token name="@shared_options@">
16 <![CDATA[ 11 <![CDATA[
17 #if $kmer: 12 #if $kmer:
18 --kmer '${kmer}' 13 --kmer ${kmer}
19 #end if 14 #end if
20 #if $expected_depth: 15 #if $expected_depth:
21 --expected_depth '${expected_depth}' 16 --expected_depth ${expected_depth}
22 #end if 17 #end if
18 $ont
19 $report_all_calls
20 #if $expected_error_rate:
21 --expected_error_rate ${expected_error_rate}
22 #end if
23 #if $min_variant_conf:
24 --min_variant_conf ${min_variant_conf}
25 #end if
26 #if $min_gene_conf:
27 --min_gene_conf ${min_gene_conf}
28 #end if
29 #if $min_proportion_expected_depth:
30 --min_proportion_expected_depth ${min_proportion_expected_depth}
31 #end if
32 #if $min_gene_percent_covg_threshold:
33 --min_gene_percent_covg_threshold ${min_gene_percent_covg_threshold}
34 #end if
35 $guess_sequence_method
36 $ignore_minor_calls
37 #if $ignore_filtered:
38 --ignore_filtered '${ignore_filtered}'
39 #end if
40 #if $model:
41 --model '${model}'
42 #end if
43 #if $ploidy:
44 --ploidy '${ploidy}'
45 #end if
46 ]]>
47 </token>
23 48
24 $ont 49 <xml name="inputs">
50 <conditional name="data_type">
51 <param name="type" type="select" label="Specify the read type.">
52 <option value="single">Single-end Data</option>
53 <option value="paired">Paired-end Data</option>
54 <option value="collection">Collection Paired-end Data</option>
55 </param>
56 <when value="single">
57 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
58 </when>
59 <when value="paired">
60 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
61 <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
62 </when>
63 <when value="collection">
64 <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
65 </when>
66 </conditional>
67 </xml>
25 68
26 $report_all_calls 69 <xml name="options">
70 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
71 <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"/>
72 <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>
73 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
74 <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
75 <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>
76 <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))"/>
77 <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%)"/>
78 <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
79 <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
80 <option value="diploid">diploid</option>
81 <option value="haploid">haploid</option>
82 </param>
83 <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>
84 <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>
85 <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
86 <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"/>
87 </xml>
27 88
28 #if $expected_error_rate: 89 <token name="@ATTRIBUTION@">
29 --expected_error_rate '${expected_error_rate}' 90 <![CDATA[
30 #end if 91 **MyKrobe predict - Antibiotic resistance predictions**
92 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
93 using Bruijn graph.
94 ]]>
95 </token>
31 96
32 #if $min_variant_conf: 97 <xml name="citation">
33 --min_variant_conf '${min_variant_conf}' 98 <citations>
34 #end if 99 <citation type="doi">10.1038/ncomms10063</citation>
35 100 </citations>
36 #if $min_gene_conf: 101 </xml>
37 --min_gene_conf '${min_gene_conf}'
38 #end if
39
40 #if $min_proportion_expected_depth:
41 --min_proportion_expected_depth '${min_proportion_expected_depth}'
42 #end if
43
44 #if $min_gene_percent_covg_threshold:
45 --min_gene_percent_covg_threshold '${min_gene_percent_covg_threshold}'
46 #end if
47
48 $guess_sequence_method
49
50 $ignore_minor_calls
51
52 #if $ignore_filtered:
53 --ignore_filtered '${ignore_filtered}'
54 #end if
55
56 #if $model:
57 --model '${model}'
58 #end if
59
60 #if $ploidy:
61 --ploidy '${ploidy}'
62 #end if
63 ]]>
64 </token>
65
66 <xml name="inputs">
67 <conditional name="data_type">
68 <param name="type" type="select" label="Specify the read type.">
69 <option value="single">Single-end Data</option>
70 <option value="paired">Paired-end Data</option>
71 <option value="collection">Collection Paired-end Data</option>
72 </param>
73 <when value="single">
74 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
75 </when>
76 <when value="paired">
77 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
78 <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
79 </when>
80 <when value="collection">
81 <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
82 </when>
83 </conditional>
84 </xml>
85
86 <xml name="options">
87 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
88 <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"/>
89 <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>
90 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
91 <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
92 <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>
93 <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))"/>
94 <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%)"/>
95 <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
96 <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
97 <option value="diploid">diploid</option>
98 <option value="haploid">haploid</option>
99 </param>
100 <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>
101 <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>
102 <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
103 <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"/>
104 </xml>
105
106 <token name="@ATTRIBUTION@">
107 <![CDATA[
108
109 **MyKrobe predict - Antibiotic resistance predictions**
110
111 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
112 using Bruijn graph.
113 ]]>
114 </token>
115
116 <xml name="citation">
117 <citations>
118 <citation type="doi">10.1038/ncomms10063</citation>
119 </citations>
120 </xml>
121 </macros> 102 </macros>