Mercurial > repos > iuc > mykrobe_genotype

comparison macro.xml @ 3:7a4c104238aa draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:45:41 +0000
parents d779062514e0
children
comparison
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2:d779062514e0 3:7a4c104238aa
1 <?xml version="1.1"?>
2 <macros> 1 <macros>
3 <xml name="requirements"> 2 <token name="@TOOL_VERSION@">0.10.0</token>
4 <requirements> 3 <token name="@PROFILE@">20.09</token>
5 <requirement type="package" version="0.7.0">mykrobe</requirement> 4 <xml name="requirements">
6 </requirements> 5 <requirements>
7 </xml> 6 <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
8 <token name="@select_inputs@"> 7 </requirements>
9 <![CDATA[ 8 </xml>
10 #set $name='sample'
11 #set $type='fastq'
12 ## Adding sample name, indicate specie and inputs fastq(s) files
13 #if $data_type.type == "paired":
14 9
15 ln -s '$data_type.fastq_input1' sample_1.fastq && 10 <token name="@shared_options@">
16 ln -s '$data_type.fastq_input2' sample_2.fastq && 11 <![CDATA[
12 #if $kmer:
13 --kmer ${kmer}
14 #end if
15 #if $expected_depth:
16 --expected_depth ${expected_depth}
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>
17 48
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>
18 68
19 #elif $data_type.type == "collection": 69 <xml name="options">
20 #set $name=str($data_type.fastq_input1.name) 70 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
21 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && 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"/>
22 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && 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>
23 88
24 #elif $data_type.type == "single": 89 <token name="@ATTRIBUTION@">
90 <![CDATA[
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>
25 96
26 97 <xml name="citation">
27 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): 98 <citations>
28 ln -s '$data_type.fastq_input1' sample.fastq && 99 <citation type="doi">10.1038/ncomms10063</citation>
29 100 </citations>
30 #end if 101 </xml>
31
32 #if $data_type.fastq_input1.is_of_type('bam'):
33 ln -s '$data_type.fastq_input1' sample.bam &&
34 #set $type='bam'
35 #end if
36
37 #end if
38 ]]>
39 </token>
40
41 <token name="@shared_options@">
42 <![CDATA[
43 #if $kmer:
44 --kmer '${kmer}'
45 #end if
46 #if $expected_depth:
47 --expected_depth '${expected_depth}'
48 #end if
49
50 $ont
51
52 $report_all_calls
53
54 #if $expected_error_rate:
55 --expected_error_rate '${expected_error_rate}'
56 #end if
57
58 #if $min_variant_conf:
59 --min_variant_conf '${min_variant_conf}'
60 #end if
61
62 #if $min_gene_conf:
63 --min_gene_conf '${min_gene_conf}'
64 #end if
65
66 #if $min_proportion_expected_depth:
67 --min_proportion_expected_depth '${min_proportion_expected_depth}'
68 #end if
69
70 #if $min_gene_percent_covg_threshold:
71 --min_gene_percent_covg_threshold '${min_gene_percent_covg_threshold}'
72 #end if
73
74 $guess_sequence_method
75
76 $ignore_minor_calls
77
78 #if $ignore_filtered:
79 --ignore_filtered '${ignore_filtered}'
80 #end if
81
82 #if $model:
83 --model '${model}'
84 #end if
85
86 #if $ploidy:
87 --ploidy '${ploidy}'
88 #end if
89 ]]>
90 </token>
91
92 <xml name="inputs">
93 <conditional name="data_type">
94 <param name="type" type="select" label="Specify the read type.">
95 <option value="single">Single-end Data</option>
96 <option value="paired">Paired-end Data</option>
97 <option value="collection">Collection Paired-end Data</option>
98 </param>
99 <when value="single">
100 <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
101 </when>
102 <when value="paired">
103 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
104 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
105 </when>
106 <when value="collection">
107 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
108 </when>
109 </conditional>
110 </xml>
111
112 <xml name="options">
113 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
114 <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"/>
115 <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>
116 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
117 <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
118 <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>
119 <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))"/>
120 <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%)"/>
121 <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
122 <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
123 <option value="diploid">diploid</option>
124 <option value="haploid">haploid</option>
125 </param>
126 <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>
127 <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>
128 <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
129 <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"/>
130 </xml>
131
132 <token name="@ATTRIBUTION@">
133 <![CDATA[
134
135 **MyKrobe predict - Antibiotic resistance predictions**
136
137 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
138 using Bruijn graph.
139 ]]>
140 </token>
141
142 <xml name="citation">
143 <citations>
144 <citation type="doi">10.1038/ncomms10063</citation>
145 </citations>
146 </xml>
147 </macros> 102 </macros>