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comparison mykrobe_predict.xml @ 4:a2e3ad69ee23 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
author iuc
date Thu, 26 Aug 2021 20:38:36 +0000
parents e8405163fb4e
children
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3:e8405163fb4e 4:a2e3ad69ee23
1 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@"> 1 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0" profile="@PROFILE@">
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"><![CDATA[
8 <![CDATA[ 8 #import difflib
9 @select_inputs@ 9 #import re
10 10
11 mykrobe predict 11 mykrobe predict
12 --sample '${name}' 12 --species '${select_species.species}'
13 --species ${select_species.species} 13 --panel '${select_species.panel}'
14 --panel '${select_species.panel}'
15 14
16 #if $conf_percent_cutoff: 15 #if $conf_percent_cutoff:
17 --conf_percent_cutoff '${conf_percent_cutoff}' 16 --conf_percent_cutoff '${conf_percent_cutoff}'
18 #end if 17 #end if
19 18
20 #if $min_depth: 19 #if $min_depth:
21 --min_depth '${min_depth}' 20 --min_depth ${min_depth}
22 #end if 21 #end if
23 22
24 @shared_options@ 23 @shared_options@
25 24
26 -q 25 -q
27 -t "\${GALAXY_SLOTS:-1}" 26 -t "\${GALAXY_SLOTS:-1}"
28 27
29 --seq 28 #if $data_type.type in ["single", "paired"]:
30 #if $data_type.type == "single": 29 #set read1 = $data_type.seq1
31 $data_type.seq1 30 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
32 #elif $data_type.type == "paired": 31 #if $data_type.type == "single":
33 $data_type.seq1 $data_type.seq2 32 --sample '${read1_identifier}'
34 #elif $data_type.type == "collection": 33 --seq '${read1}'
35 $data_type.collection1.forward $data_type.collection1.reverse 34 #else:
36 #end if 35 #set read2 = $data_type.seq2
36 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
37 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
38 #set match = $matches[0]
39 #set identifier = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
40 --sample '${identifier}'
41 --seq '${read1}' '${read2}'
42 #end if
43 #elif $data_type.type == "collection":
44 #set identifier = re.sub('[^\s\w\-]', '_', str($data_type.collection1.element_identifier))
45 --sample '${identifier}'
46 --seq '${data_type.collection1.forward}' '${data_type.collection1.reverse}'
47 #end if
37 48
38 --format '${format}' 49 --format '${format}'
39 50
40 > '$output' 51 > '$output']]>
41 ]]> 52 </command>
42 </command> 53 <inputs>
43 <inputs> 54 <expand macro="inputs"/>
44 <expand macro="inputs"/> 55 <conditional name="select_species">
45 <conditional name="select_species"> 56 <param name="species" type="select" label="Specify Species for AMR">
46 <param name="species" type="select" label="Specify Species for AMR"> 57 <option value="tb">Mycobacterium tuberculosis (tb)</option>
47 <option value="tb">Mycobacterium tuberculosis (tb)</option> 58 <option value="staph">Staphylococcus aureus (staph)</option>
48 <option value="staph">Staphylococcus aureus (staph)</option> 59 <option value="sonnei">Shigella sonnei (sonnei)</option>
49 <option value="sonnei">Shigella sonnei (sonnei)</option> 60 </param>
50 </param> 61 <when value="staph">
51 <when value="staph"> 62 <param name="panel" type="select" label="Select panel for Staph only">
52 <param name="panel" type="select" label="Select panel for Staph only"> 63 <option value="20170217">20170217</option>
53 <option value="20170217">20170217</option> 64 </param>
65 </when>
66 <when value="tb">
67 <param name="panel" type="select" label="Select panel for TB only">
68 <option value="202010">202010</option>
69 <option value="201901">201901</option>
70 <option value="bradley-2015">Bradely 2015</option>
71 </param>
72 </when>
73 <when value="sonnei">
74 <param name="panel" type="select" label="Select panel for sonnei only">
75 <option value="20210201">20210201</option>
76 <option value="20201012">20201012</option>
77 </param>
78 </when>
79 </conditional>
80 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/>
81 <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">
82 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
54 </param> 83 </param>
55 </when> 84 <expand macro="options"/>
56 <when value="tb"> 85 <param argument="--format" type="select" label="Select the prefered output format">
57 <param name="panel" type="select" label="Select panel for TB only"> 86 <option value="csv" >csv</option>
58 <option value="202010">202010</option> 87 <option value="json">json</option>
59 <option value="201901">201901</option>
60 <option value="bradley-2015">Bradely 2015</option>
61 </param> 88 </param>
62 </when> 89 </inputs>
63 <when value="sonnei"> 90 <outputs>
64 <param name="panel" type="select" label="Select panel for sonnei only"> 91 <data name="output" format="csv" label="prediction">
65 <option value="20210201">20210201</option> 92 <change_format>
66 <option value="20201012">20201012</option> 93 <when input="format" value="json" format="json"/>
67 </param> 94 </change_format>
68 </when> 95 </data>
69 </conditional> 96 </outputs>
70 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/> 97 <tests>
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"> 98 <test>
72 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" /> 99 <param name="type" value="single"/>
73 </param> 100 <param name="seq1" ftype="fastq" value="reads.fastq"/>
74 <expand macro="options"/> 101 <param name="species" value="tb"/>
75 <param argument="--format" type="select" label="Select the prefered output format"> 102 <param name="panel" value="bradley-2015"/>
76 <option value="csv" >csv</option> 103 <param name="format" value="json"/>
77 <option value="json">json</option> 104 <output name="output">
78 </param> 105 <assert_contents>
79 </inputs> 106 <has_text_matching expression="susceptibility"/>
80 <outputs> 107 </assert_contents>
81 <data name="output" format="csv" label="prediction"> 108 </output>
82 <change_format> 109 </test>
83 <when input="format" value="json" format="json"/> 110 <test>
84 </change_format> 111 <param name="type" value="single"/>
85 </data> 112 <param name="seq1" ftype="fastq" value="reads.fastq"/>
86 </outputs> 113 <param name="species" value="sonnei"/>
87 <tests> 114 <param name="panel" value="20201012"/>
88 <test> 115 <param name="format" value="json"/>
89 <param name="type" value="single"/> 116 <output name="output">
90 <param name="seq1" ftype="fastq" value="reads.fastq"/> 117 <assert_contents>
91 <param name="species" value="tb"/> 118 <has_text_matching expression="susceptibility"/>
92 <param name="panel" value="bradley-2015"/> 119 </assert_contents>
93 <param name="format" value="json"/> 120 </output>
94 <output name="output"> 121 </test>
95 <assert_contents> 122 <test>
96 <has_text_matching expression="susceptibility"/> 123 <param name="type" value="single"/>
97 </assert_contents> 124 <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>
98 </output> 125 <param name="species" value="sonnei"/>
99 </test> 126 <param name="panel" value="20201012"/>
100 <test> 127 <param name="format" value="json"/>
101 <param name="type" value="single"/> 128 <output name="output">
102 <param name="seq1" ftype="fastq" value="reads.fastq"/> 129 <assert_contents>
103 <param name="species" value="sonnei"/> 130 <has_text_matching expression="susceptibility"/>
104 <param name="panel" value="20201012"/> 131 </assert_contents>
105 <param name="format" value="json"/> 132 </output>
106 <output name="output"> 133 </test>
107 <assert_contents> 134 </tests>
108 <has_text_matching expression="susceptibility"/> 135 <help>
109 </assert_contents> 136 @ATTRIBUTION@
110 </output> 137 </help>
111 </test> 138 <expand macro="citation" />
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"/>
117 <param name="format" value="json"/>
118 <output name="output">
119 <assert_contents>
120 <has_text_matching expression="susceptibility"/>
121 </assert_contents>
122 </output>
123 </test>
124 </tests>
125 <help>
126 @ATTRIBUTION@
127 </help>
128 <expand macro="citation" />
129 </tool> 139 </tool>
140