Mercurial > repos > iuc > mykrobe_predict
comparison mykrobe_predict.xml @ 1:60ffb465aa4d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
author | iuc |
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date | Tue, 02 Apr 2019 11:56:45 -0400 |
parents | 33463c79e697 |
children | cedd631dc124 |
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0:33463c79e697 | 1:60ffb465aa4d |
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1 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.5.6" > | 1 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.6.1"> |
2 <description>Antibiotic resistance predictions</description> | 2 <description>Antibiotic resistance predictions</description> |
3 <macros> | 3 <macros> |
4 <import>macro.xml</import> | 4 <import>macro.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <command detect_errors="exit_code"> | 7 <command detect_errors="exit_code"> |
8 <![CDATA[ | 8 <![CDATA[ |
9 @select_inputs@ | 9 @select_inputs@ |
10 | 10 |
11 mykrobe predict | 11 mykrobe predict |
12 '$name' | 12 '${name}' |
13 $select_species.species | 13 ${select_species.species} |
14 | 14 |
15 | 15 #if $select_species.panel == 'custom': |
16 #if $select_species.species =='tb': | 16 #if $adv.custom_probe: |
17 --panel $select_species.panel | 17 --custom_probe_set_path '${adv.custom_probe}' |
18 #end if | |
19 #if $adv.custom_variant_to_resistance: | |
20 --custom_variant_to_resistance_json '${adv.custom_variant_to_resistance}' | |
21 #end if | |
22 #elif $select_species.panel: | |
23 --panel '${select_species.panel}' | |
18 #end if | 24 #end if |
19 | 25 |
20 | 26 #if $conf_percent_cutoff: |
21 | 27 --conf_percent_cutoff '${conf_percent_cutoff}' |
22 #if $kmer: | |
23 --kmer $kmer | |
24 #end if | 28 #end if |
25 | 29 |
26 #if $min_variant_conf: | 30 #if $min_depth: |
27 --min_variant_conf $min_variant_conf | 31 --min_depth '${min_depth}' |
28 #end if | 32 #end if |
29 | 33 |
34 @shared_options@ | |
30 | 35 |
31 #if $expected_depth: | |
32 --expected_depth $expected_depth | |
33 #end if | |
34 | |
35 | |
36 #if $min_gene_conf: | |
37 --min_gene_conf $min_gene_conf | |
38 #end if | |
39 | |
40 | |
41 | |
42 #if $min_gene_percent_covg_threshold: | |
43 --min_gene_percent_covg_threshold $min_gene_percent_covg_threshold | |
44 #end if | |
45 | |
46 | |
47 #if $min_depth: | |
48 --min_depth $min_depth | |
49 #end if | |
50 | |
51 | |
52 #if $expected_error_rate: | |
53 --expected_error_rate $expected_error_rate | |
54 #end if | |
55 | |
56 $report_all_calls | |
57 | |
58 $ont | |
59 -q | 36 -q |
60 -t "\${GALAXY_SLOTS:-1}" | 37 -t "\${GALAXY_SLOTS:-1}" |
61 | 38 |
62 -1 | 39 -1 |
63 #if $type == 'fastq': | 40 #if $type == 'fastq': |
64 *.fastq | 41 *.fastq |
65 #else | 42 #else |
66 *.bam | 43 *.bam |
67 #end if | 44 #end if |
68 > $json | 45 |
46 --format '${format}' | |
47 | |
48 > '$output' | |
69 ]]> | 49 ]]> |
70 </command> | 50 </command> |
71 <inputs> | 51 <inputs> |
72 <expand macro="inputs" /> | 52 <expand macro="inputs"/> |
73 <conditional name="select_species"> | 53 <conditional name="select_species"> |
74 <param name="species" type="select" label="Specify Species for AMR"> | 54 <param name="species" type="select" label="Specify Species for AMR"> |
75 <option value="tb">Mycobacterium tuberculosis (tb)</option> | 55 <option value="tb">Mycobacterium tuberculosis (tb)</option> |
76 <option value="staph">Staphylococcus aureus (staph)</option> | 56 <option value="staph">Staphylococcus aureus (staph)</option> |
77 </param> | 57 </param> |
78 <when value="staph"/> | 58 <when value="staph"> |
59 <param name="panel" type="select" optional="true" label="Select panel for Staph only"> | |
60 <option value="custom">Custom</option> | |
61 </param> | |
62 </when> | |
79 <when value="tb"> | 63 <when value="tb"> |
80 <param name="panel" type="select" label="Select panel for TB only"> | 64 <param name="panel" type="select" label="Select panel for TB only"> |
65 <option value="201901">201901</option> | |
81 <option value="bradley-2015">Bradely 2015</option> | 66 <option value="bradley-2015">Bradely 2015</option> |
82 <option value="walker-2015">Walker 2015</option> | 67 <option value="walker-2015">Walker 2015</option> |
68 <option value="custom">Custom</option> | |
83 </param> | 69 </param> |
84 </when> | 70 </when> |
85 </conditional> | 71 </conditional> |
86 <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/> | 72 <section name="adv" title="Custom Panel" expanded="false"> |
87 <param name="expected_error_rate" argument="--expected_error_rate" optional="True" type="float" label="Expected Error Rate" help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/> | 73 <param name="custom_probe" type="data" format="fasta" label="Custom Probe" optional="True" help="Don't include filtered genotypes"/> |
88 <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth" help=""/> | 74 <param name="custom_variant_to_resistance" type="data" format="json" label="Custom Variant to Resistance" optional="True" help="JSON file with key,value pairs of variant names and induced drug resistance."/> |
89 <param name="min_depth" argument="--min_depth" optional="True" type="integer" min="0" label="Minimum Depth" help=""/> | 75 </section> |
90 <param name="report_all_calls" argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="report all calls" help=""/> | 76 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/> |
91 <param name="ont" argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/> | 77 <param argument="--conf_percent_cutoff" optional="True" type="integer" label="Confidence percent cutoff" help="Number between 0 and 100. Determines --min_variant_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff"> |
92 <param name="min_variant_conf" argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/> | 78 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" /> |
93 <param name="min_gene_conf" argument="--min_gene_conf" optional="True" type="integer" min="0" label="minimum genotype confidence for gene genotyping" help=""/> | 79 </param> |
94 <param name="min_gene_percent_covg_threshold" 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 allelesreported))"/> | 80 <expand macro="options"/> |
81 <param argument="--format" type="select" label="Select the prefered output format"> | |
82 <option value="csv" >csv</option> | |
83 <option value="json">json</option> | |
84 </param> | |
95 </inputs> | 85 </inputs> |
96 | |
97 <outputs> | 86 <outputs> |
98 <data name="json" format="json" label="JSON prediction"/> | 87 <data name="output" format="csv" label="prediction"> |
88 <change_format> | |
89 <when input="format" value="json" format="json"/> | |
90 </change_format> | |
91 </data> | |
99 </outputs> | 92 </outputs> |
100 <tests> | 93 <tests> |
101 <test> | 94 <test> |
102 <param name="type" value="single"/> | 95 <param name="type" value="single"/> |
103 <param name="fastq_input1" value="reads.fastq"/> | 96 <param name="fastq_input1" value="reads.fastq"/> |
104 <param name="species" value="tb"/> | 97 <param name="species" value="tb"/> |
105 <param name="panel" value="bradley-2015"/> | 98 <param name="panel" value="bradley-2015"/> |
106 <output name="json"> | 99 <param name="format" value="json"/> |
100 <output name="output"> | |
107 <assert_contents> | 101 <assert_contents> |
108 <has_text_matching expression="variant_calls"/> | 102 <has_text_matching expression="susceptibility"/> |
109 </assert_contents> | 103 </assert_contents> |
110 </output> | 104 </output> |
111 </test> | 105 </test> |
112 </tests> | 106 </tests> |
113 <help> | 107 <help> |