Mercurial > repos > iuc > mykrobe_predict

comparison mykrobe_predict.xml @ 3:e8405163fb4e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 2b9fb5d1f0ffb7ecd51561d3e325813c4f8e7f3e"
author iuc
date Tue, 10 Aug 2021 11:29:58 +0000
parents cedd631dc124
children a2e3ad69ee23
comparison
equal deleted inserted replaced
2:cedd631dc124 3:e8405163fb4e
1 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.7.0"> 1 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@">
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 '${name}' 12 --sample '${name}'
13 ${select_species.species} 13 --species ${select_species.species}
14 14 --panel '${select_species.panel}'
15 #if $select_species.panel == 'custom':
16 #if $adv.custom_probe:
17 --custom_probe_set_path '${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}'
24 #end if
25 15
26 #if $conf_percent_cutoff: 16 #if $conf_percent_cutoff:
27 --conf_percent_cutoff '${conf_percent_cutoff}' 17 --conf_percent_cutoff '${conf_percent_cutoff}'
28 #end if 18 #end if
29 19
34 @shared_options@ 24 @shared_options@
35 25
36 -q 26 -q
37 -t "\${GALAXY_SLOTS:-1}" 27 -t "\${GALAXY_SLOTS:-1}"
38 28
39 -1 29 --seq
40 #if $type == 'fastq': 30 #if $data_type.type == "single":
41 *.fastq 31 $data_type.seq1
42 #else 32 #elif $data_type.type == "paired":
43 *.bam 33 $data_type.seq1 $data_type.seq2
44 #end if 34 #elif $data_type.type == "collection":
35 $data_type.collection1.forward $data_type.collection1.reverse
36 #end if
45 37
46 --format '${format}' 38 --format '${format}'
47 39
48 > '$output' 40 > '$output'
49 ]]> 41 ]]>
52 <expand macro="inputs"/> 44 <expand macro="inputs"/>
53 <conditional name="select_species"> 45 <conditional name="select_species">
54 <param name="species" type="select" label="Specify Species for AMR"> 46 <param name="species" type="select" label="Specify Species for AMR">
55 <option value="tb">Mycobacterium tuberculosis (tb)</option> 47 <option value="tb">Mycobacterium tuberculosis (tb)</option>
56 <option value="staph">Staphylococcus aureus (staph)</option> 48 <option value="staph">Staphylococcus aureus (staph)</option>
49 <option value="sonnei">Shigella sonnei (sonnei)</option>
57 </param> 50 </param>
58 <when value="staph"> 51 <when value="staph">
59 <param name="panel" type="select" optional="true" label="Select panel for Staph only"> 52 <param name="panel" type="select" label="Select panel for Staph only">
60 <option value="custom">Custom</option> 53 <option value="20170217">20170217</option>
61 </param> 54 </param>
62 </when> 55 </when>
63 <when value="tb"> 56 <when value="tb">
64 <param name="panel" type="select" label="Select panel for TB only"> 57 <param name="panel" type="select" label="Select panel for TB only">
58 <option value="202010">202010</option>
65 <option value="201901">201901</option> 59 <option value="201901">201901</option>
66 <option value="bradley-2015">Bradely 2015</option> 60 <option value="bradley-2015">Bradely 2015</option>
67 <option value="walker-2015">Walker 2015</option> 61 </param>
68 <option value="custom">Custom</option> 62 </when>
63 <when value="sonnei">
64 <param name="panel" type="select" label="Select panel for sonnei only">
65 <option value="20210201">20210201</option>
66 <option value="20201012">20201012</option>
69 </param> 67 </param>
70 </when> 68 </when>
71 </conditional> 69 </conditional>
72 <section name="adv" title="Custom Panel" expanded="false">
73 <param name="custom_probe" type="data" format="fasta" label="Custom Probe" optional="True" help="Don't include filtered genotypes"/>
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."/>
75 </section>
76 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/> 70 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" 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"> 71 <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">
78 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" /> 72 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
79 </param> 73 </param>
80 <expand macro="options"/> 74 <expand macro="options"/>
91 </data> 85 </data>
92 </outputs> 86 </outputs>
93 <tests> 87 <tests>
94 <test> 88 <test>
95 <param name="type" value="single"/> 89 <param name="type" value="single"/>
96 <param name="fastq_input1" value="reads.fastq"/> 90 <param name="seq1" ftype="fastq" value="reads.fastq"/>
97 <param name="species" value="tb"/> 91 <param name="species" value="tb"/>
98 <param name="panel" value="bradley-2015"/> 92 <param name="panel" value="bradley-2015"/>
93 <param name="format" value="json"/>
94 <output name="output">
95 <assert_contents>
96 <has_text_matching expression="susceptibility"/>
97 </assert_contents>
98 </output>
99 </test>
100 <test>
101 <param name="type" value="single"/>
102 <param name="seq1" ftype="fastq" value="reads.fastq"/>
103 <param name="species" value="sonnei"/>
104 <param name="panel" value="20201012"/>
105 <param name="format" value="json"/>
106 <output name="output">
107 <assert_contents>
108 <has_text_matching expression="susceptibility"/>
109 </assert_contents>
110 </output>
111 </test>
112 <test>
113 <param name="type" value="single"/>
114 <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>
115 <param name="species" value="sonnei"/>
116 <param name="panel" value="20201012"/>
99 <param name="format" value="json"/> 117 <param name="format" value="json"/>
100 <output name="output"> 118 <output name="output">
101 <assert_contents> 119 <assert_contents>
102 <has_text_matching expression="susceptibility"/> 120 <has_text_matching expression="susceptibility"/>
103 </assert_contents> 121 </assert_contents>