Mercurial > repos > iuc > mykrobe_predict

comparison macro.xml @ 1:9b5743b8208f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
author iuc
date Tue, 02 Apr 2019 11:55:20 -0400
parents 32f8ee6a4712
children 8782fc7296b2
comparison
equal deleted inserted replaced
0:32f8ee6a4712 1:9b5743b8208f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.5.6">mykrobe</requirement> 5 <requirement type="package" version="0.6.1">mykrobe</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8
9 <token name="@select_inputs@"> 8 <token name="@select_inputs@">
10 <![CDATA[ 9 <![CDATA[
11 #set $name='sample' 10 #set $name='sample'
12 #set $type='fastq' 11 #set $type='fastq'
13 ## Adding sample name, indicate specie and inputs fastq(s) files 12 ## Adding sample name, indicate specie and inputs fastq(s) files
37 36
38 #end if 37 #end if
39 ]]> 38 ]]>
40 </token> 39 </token>
41 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
42 <xml name="inputs"> 92 <xml name="inputs">
43 <conditional name="data_type"> 93 <conditional name="data_type">
44 <param name="type" type="select" label="Specify the read type."> 94 <param name="type" type="select" label="Specify the read type.">
45 <option value="single">Single-end Data</option> 95 <option value="single">Single-end Data</option>
46 <option value="paired">Paired-end Data</option> 96 <option value="paired">Paired-end Data</option>
57 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> 107 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
58 </when> 108 </when>
59 </conditional> 109 </conditional>
60 </xml> 110 </xml>
61 111
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
62 <token name="@ATTRIBUTION@"> 132 <token name="@ATTRIBUTION@">
63 <![CDATA[ 133 <![CDATA[
64 134
65 **MyKrobe predict - Antibiotic resistance predictions** 135 **MyKrobe predict - Antibiotic resistance predictions**
66 136