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comparison mykrobe_predict.xml @ 0:33463c79e697 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
author iuc
date Sat, 13 Jan 2018 09:02:31 -0500
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children 60ffb465aa4d
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-1:000000000000 0:33463c79e697
1 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.5.6" >
2 <description>Antibiotic resistance predictions</description>
3 <macros>
4 <import>macro.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 @select_inputs@
10
11 mykrobe predict
12 '$name'
13 $select_species.species
14
15
16 #if $select_species.species =='tb':
17 --panel $select_species.panel
18 #end if
19
20
21
22 #if $kmer:
23 --kmer $kmer
24 #end if
25
26 #if $min_variant_conf:
27 --min_variant_conf $min_variant_conf
28 #end if
29
30
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
60 -t "\${GALAXY_SLOTS:-1}"
61
62 -1
63 #if $type == 'fastq':
64 *.fastq
65 #else
66 *.bam
67 #end if
68 > $json
69 ]]>
70 </command>
71 <inputs>
72 <expand macro="inputs" />
73 <conditional name="select_species">
74 <param name="species" type="select" label="Specify Species for AMR">
75 <option value="tb">Mycobacterium tuberculosis (tb)</option>
76 <option value="staph">Staphylococcus aureus (staph)</option>
77 </param>
78 <when value="staph"/>
79 <when value="tb">
80 <param name="panel" type="select" label="Select panel for TB only">
81 <option value="bradley-2015">Bradely 2015</option>
82 <option value="walker-2015">Walker 2015</option>
83 </param>
84 </when>
85 </conditional>
86 <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
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"/>
88 <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth" help=""/>
89 <param name="min_depth" argument="--min_depth" optional="True" type="integer" min="0" label="Minimum Depth" help=""/>
90 <param name="report_all_calls" argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="report all calls" help=""/>
91 <param name="ont" argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
92 <param name="min_variant_conf" argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
93 <param name="min_gene_conf" argument="--min_gene_conf" optional="True" type="integer" min="0" label="minimum genotype confidence for gene genotyping" help=""/>
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))"/>
95 </inputs>
96
97 <outputs>
98 <data name="json" format="json" label="JSON prediction"/>
99 </outputs>
100 <tests>
101 <test>
102 <param name="type" value="single"/>
103 <param name="fastq_input1" value="reads.fastq"/>
104 <param name="species" value="tb"/>
105 <param name="panel" value="bradley-2015"/>
106 <output name="json">
107 <assert_contents>
108 <has_text_matching expression="variant_calls"/>
109 </assert_contents>
110 </output>
111 </test>
112 </tests>
113 <help>
114 @ATTRIBUTION@
115 </help>
116 <expand macro="citation" />
117 </tool>