Mercurial > repos > bvalot > pymlst
comparison wgmlst_add.xml @ 0:a3cc35af3635 draft
planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author | bvalot |
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date | Thu, 16 Jun 2022 12:32:28 +0000 |
parents | |
children | 5b2c48fa0175 |
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-1:000000000000 | 0:a3cc35af3635 |
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1 <tool id="wgmlst_add_wrapper" name="Add strain to cg/wgMLST database" version="2.1.3"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="2.1.3">pymlst</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" level="fatal" /> | |
8 </stdio> | |
9 <version_command>wgMLST -v</version_command> | |
10 <command><![CDATA[ | |
11 cp '${database}' '${databaseout}' && | |
12 wgMLST | |
13 #if $data.input == "fasta" | |
14 add | |
15 #else | |
16 add2 | |
17 #end if | |
18 #if str($coverage) | |
19 -c $coverage | |
20 #end if | |
21 #if str($identity) | |
22 -i $identity | |
23 #end if | |
24 #if $data.input == "fasta" | |
25 #if $strain | |
26 -s '$strain' | |
27 #else | |
28 -s '$data.fastain.name.replace(" ", "_").replace("-", "_")' | |
29 #end if | |
30 '${databaseout}' '${data.fastain}' | |
31 #end if | |
32 #if $data.input == "fastqsingle" | |
33 #if str($data.reads) | |
34 -r $data.reads | |
35 #end if | |
36 #if $strain | |
37 -s '$strain' | |
38 #else | |
39 -s '$data.single.name.replace(" ", "_").replace("-", "_")' | |
40 #end if | |
41 '${databaseout}' '${data.single}' | |
42 #end if | |
43 #if $data.input == "fastqpaired" | |
44 #if str($data.reads) | |
45 -r $data.reads | |
46 #end if | |
47 #if $strain | |
48 -s '$strain' | |
49 #else | |
50 -s '$data.forward.name.replace(" ", "_").replace("-", "_")' | |
51 #end if | |
52 '${databaseout}' '${data.forward}' '${data.reverse}' | |
53 #end if | |
54 #if $data.input == "fastqpaired2" | |
55 #if str($data.reads) | |
56 -r $data.reads | |
57 #end if | |
58 #if $strain | |
59 -s '$strain' | |
60 #else | |
61 -s '$data.pairedfile.name.replace(" ", "_").replace("-", "_")' | |
62 #end if | |
63 '${databaseout}' '${data.pairedfile.forward}' | |
64 '${data.pairedfile.reverse}' | |
65 #end if | |
66 #if $log | |
67 2> '${logfile}' | |
68 #end if | |
69 ]]> | |
70 </command> | |
71 <inputs> | |
72 <param name="database" type="data" | |
73 format="sqlite" | |
74 label="cg/wgMLST database" | |
75 help="Sqlite format from cg/wgMLST database" /> | |
76 <conditional name="data"> | |
77 <param name="input" type="select" label="Select type of data"> | |
78 <option value="fasta" selected="true">Assembly (fasta)</option> | |
79 <option value="fastqsingle">Raw data (single)</option> | |
80 <option value="fastqpaired">Raw data (paired separated)</option> | |
81 <option value="fastqpaired2">Raw data (paired)</option> | |
82 </param> | |
83 <when value="fasta"> | |
84 <param name="fastain" type="data" format="fasta" | |
85 label="Assembly Genome" help="Fasta format" /> | |
86 </when> | |
87 <when value="fastqsingle"> | |
88 <param name="single" type="data" format="fastq,fastq.gz" | |
89 label="Single read file" help="Fastq(gz) format" /> | |
90 <param name="reads" type="integer" value="10" optional="true" | |
91 label="Minimum reads coverage to search gene" /> | |
92 </when> | |
93 <when value="fastqpaired"> | |
94 <param name="forward" type="data" format="fastq,fastq.gz" | |
95 label="Forward read file" help="Fastq(gz) format" /> | |
96 <param name="reverse" type="data" format="fastq,fastq.gz" | |
97 label="Reverse read file" help="Fastq(gz) format" /> | |
98 <param name="reads" type="integer" value="10" optional="true" | |
99 label="Minimum reads coverage to search gene" /> | |
100 </when> | |
101 <when value="fastqpaired2"> | |
102 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz" | |
103 label="Paired of read files" help="Fastq(gz) format" | |
104 collection_type="paired" /> | |
105 <param name="reads" type="integer" value="10" optional="true" | |
106 label="Minimum reads coverage to search gene" /> | |
107 </when> | |
108 </conditional> | |
109 <param name="strain" type="text" value="" size="50" | |
110 optional="false" | |
111 label="Strain" | |
112 help="Name of the strain"> | |
113 <sanitizer invalid_char="_" > | |
114 <valid initial="string.ascii_letters,string.digits"> | |
115 <add value="_" /> | |
116 <add value="." /> | |
117 </valid> | |
118 </sanitizer> | |
119 </param> | |
120 <param name="identity" type="float" value="0.9" optional="false" | |
121 label="Identity" | |
122 help="Minimum identity to search gene" /> | |
123 <param name="coverage" type="float" value="0.9" optional="false" | |
124 label="Coverage" | |
125 help="Minimum coverage to search gene" /> | |
126 <param name="log" type="boolean" checked="true" | |
127 label="Write log file" /> | |
128 </inputs> | |
129 <outputs> | |
130 <data name="databaseout" format="sqlite" label="${database.name}"> | |
131 </data> | |
132 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log"> | |
133 <filter>log</filter> | |
134 </data> | |
135 </outputs> | |
136 <tests> | |
137 <test expect_num_outputs="2"> | |
138 <param name="database" value="wgmlst_ecoli.db" /> | |
139 <conditional name="data"> | |
140 <param name="input" value="fasta" /> | |
141 <param name="fastain" ftype="fasta" value="EHSB-021.fasta" /> | |
142 </conditional> | |
143 <param name="identity" value="0.8" /> | |
144 <output name="logfile" ftype="txt"> | |
145 <assert_contents> | |
146 <has_text text="Added 2497 new MLST genes to the database" /> | |
147 <has_text text="Found 32 partial genes, filled 30" /> | |
148 <has_text text="Removed 4 genes" /> | |
149 </assert_contents> | |
150 </output> | |
151 </test> | |
152 <!-- <test expect_num_outputs="2"> --> | |
153 <!-- <param name="database" value="wgmlst_ecoli.db" /> --> | |
154 <!-- <param name="strain" value="EHSB-021" /> --> | |
155 <!-- <conditional name="data"> --> | |
156 <!-- <param name="input" value="fastqpaired" /> --> | |
157 <!-- <param name="forward" ftype="fastq.gz" value="EHSB-021_R1.fastq.gz" /> --> | |
158 <!-- <param name="reverse" ftype="fastq.gz" value="EHSB-021_R2.fastq.gz" /> --> | |
159 <!-- <param name="reads" value="5" /> --> | |
160 <!-- </conditional> --> | |
161 <!-- <output name="logfile" ftype="txt"> --> | |
162 <!-- <assert_contents> --> | |
163 <!-- <has_text_matching expression="Add 24\d\d new MLST genes to database" /> --> | |
164 <!-- <has_text_matching expression="Remove \d genes with uncertain bases" /> --> | |
165 <!-- <has_text_matching expression="Remove \d\d genes with bad CDS" /> --> | |
166 <!-- </assert_contents> --> | |
167 <!-- </output> --> | |
168 <!-- </test> --> | |
169 </tests> | |
170 <help> | |
171 **What it does** | |
172 | |
173 Add a Strain to the cg/wgMLST database | |
174 | |
175 You can use | |
176 - Genome assembly (blat search) | |
177 - Raw data (kma search) | |
178 | |
179 **Options:** | |
180 -s, --strain TEXT Name of the strain (default:genome name). | |
181 -i, --identity FLOAT Minimum identity to search gene (default=0.9). | |
182 -c, --coverage FLOAT Minimum coverage to search gene (default=0.95). | |
183 -r, --reads INTEGER Minimum reads coverage to search gene (default=10). | |
184 -f, --fasta FILENAME Write fasta file with gene allele. | |
185 | |
186 **License and citation** | |
187 | |
188 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`. | |
189 </help> | |
190 <citations> | |
191 </citations> | |
192 </tool> |