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comparison mykrobe_predict.xml.orig @ 5:db95e63ac3fb draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:46:02 +0000
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4:70a3a5377e6d 5:db95e63ac3fb
1 <<<<<<< HEAD
2 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0" profile="@PROFILE@">
3 <description>Antibiotic resistance predictions</description>
4 =======
5 <tool id="mykrobe_predict" name="mkyrobe predict" version="0.7.0">
6 <description>Antibiotic resistance predictions</description>
7 <xrefs>
8 <xref type='bio.tools'>Mykrobe</xref>
9 </xrefs>
10 >>>>>>> 84b0f9990 (add bio.tools IDs until M)
11 <macros>
12 <import>macro.xml</import>
13 </macros>
14 <expand macro="requirements"/>
15 <<<<<<< HEAD
16 <command detect_errors="exit_code"><![CDATA[
17 #import difflib
18 #import re
19 =======
20 <command detect_errors="exit_code">
21 <![CDATA[
22 @select_inputs@
23 >>>>>>> 84b0f9990 (add bio.tools IDs until M)
24
25 mykrobe predict
26 --species '${select_species.species}'
27 --panel '${select_species.panel}'
28
29 #if $conf_percent_cutoff:
30 --conf_percent_cutoff '${conf_percent_cutoff}'
31 #end if
32
33 #if $min_depth:
34 --min_depth ${min_depth}
35 #end if
36
37 @shared_options@
38
39 -q
40 -t "\${GALAXY_SLOTS:-1}"
41
42 #if $data_type.type in ["single", "paired"]:
43 #set read1 = $data_type.seq1
44 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
45 #if $data_type.type == "single":
46 --sample '${read1_identifier}'
47 --seq '${read1}'
48 #else:
49 #set read2 = $data_type.seq2
50 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
51 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
52 #set match = $matches[0]
53 #set identifier = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
54 --sample '${identifier}'
55 --seq '${read1}' '${read2}'
56 #end if
57 #elif $data_type.type == "collection":
58 #set identifier = re.sub('[^\s\w\-]', '_', str($data_type.collection1.element_identifier))
59 --sample '${identifier}'
60 --seq '${data_type.collection1.forward}' '${data_type.collection1.reverse}'
61 #end if
62
63 --format '${format}'
64
65 > '$output']]>
66 </command>
67 <inputs>
68 <expand macro="inputs"/>
69 <conditional name="select_species">
70 <param name="species" type="select" label="Specify Species for AMR">
71 <option value="tb">Mycobacterium tuberculosis (tb)</option>
72 <option value="staph">Staphylococcus aureus (staph)</option>
73 <option value="sonnei">Shigella sonnei (sonnei)</option>
74 </param>
75 <when value="staph">
76 <param name="panel" type="select" label="Select panel for Staph only">
77 <option value="20170217">20170217</option>
78 </param>
79 </when>
80 <when value="tb">
81 <param name="panel" type="select" label="Select panel for TB only">
82 <option value="202010">202010</option>
83 <option value="201901">201901</option>
84 <option value="bradley-2015">Bradely 2015</option>
85 </param>
86 </when>
87 <when value="sonnei">
88 <param name="panel" type="select" label="Select panel for sonnei only">
89 <option value="20210201">20210201</option>
90 <option value="20201012">20201012</option>
91 </param>
92 </when>
93 </conditional>
94 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/>
95 <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">
96 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
97 </param>
98 <expand macro="options"/>
99 <param argument="--format" type="select" label="Select the prefered output format">
100 <option value="csv" >csv</option>
101 <option value="json">json</option>
102 </param>
103 </inputs>
104 <outputs>
105 <data name="output" format="csv" label="prediction">
106 <change_format>
107 <when input="format" value="json" format="json"/>
108 </change_format>
109 </data>
110 </outputs>
111 <tests>
112 <test>
113 <param name="type" value="single"/>
114 <param name="seq1" ftype="fastq" value="reads.fastq"/>
115 <param name="species" value="tb"/>
116 <param name="panel" value="bradley-2015"/>
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 <test>
125 <param name="type" value="single"/>
126 <param name="seq1" ftype="fastq" value="reads.fastq"/>
127 <param name="species" value="sonnei"/>
128 <param name="panel" value="20201012"/>
129 <param name="format" value="json"/>
130 <output name="output">
131 <assert_contents>
132 <has_text_matching expression="susceptibility"/>
133 </assert_contents>
134 </output>
135 </test>
136 <test>
137 <param name="type" value="single"/>
138 <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>
139 <param name="species" value="sonnei"/>
140 <param name="panel" value="20201012"/>
141 <param name="format" value="json"/>
142 <output name="output">
143 <assert_contents>
144 <has_text_matching expression="susceptibility"/>
145 </assert_contents>
146 </output>
147 </test>
148 </tests>
149 <help>
150 @ATTRIBUTION@
151 </help>
152 <expand macro="citation" />
153 </tool>
154