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comparison wgmlst_export.xml @ 0:a3cc35af3635 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author bvalot
date Thu, 16 Jun 2022 12:32:28 +0000
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-1:000000000000 0:a3cc35af3635
1 <tool id="wgmlst_export_wrapper" name="Export result of 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>
11 wgMLST
12 #if $export_result.export == "distance"
13 distance
14 #end if
15 #if $export_result.export == "mlst"
16 mlst
17 #end if
18 #if $export_result.export == "strain"
19 strain
20 #if $export_result.count
21 -c
22 #end if
23 #end if
24 #if $export_result.export == "gene"
25 gene
26 #end if
27 #if str($mincover)
28 -m $mincover
29 #end if
30 #if $keep
31 -k
32 #end if
33 #if $inverse
34 -V
35 #end if
36 #if $duplicate
37 -d
38 #end if
39 '${database}'
40 > '${$output}'
41 #if $log
42 2> '${logfile}'
43 #end if
44 </command>
45 <inputs>
46 <param name="database" type="data"
47 format="sqlite"
48 label="cg/wgMLST database"
49 help="Sqlite format from cg/wgMLST database" />
50 <conditional name="export_result">
51 <param name="export" type="select" label="Select the data export">
52 <option value="distance">Distance matrix between strains on the cg/wgMLST database</option>
53 <option value="mlst">cg/wgMLST table for each strain on the cg/wgMLST database</option>
54 <option value="strain">List of the strains on the cg/wgMLST database</option>
55 <option value="gene">List of the genes on the cg/wgMLST database</option>
56 </param>
57 <when value="strain">
58 <param name="count" type="boolean" checked="false"
59 label="Report the number of gene found for each strain" />
60 </when>
61 <when value="distance" />
62 <when value="mlst" />
63 <when value="gene" />
64 </conditional>
65 <param name="mincover" type="integer" value="0"
66 optional="true"
67 label="Minimun number of strain found to keep a gene" />
68 <param name="keep" type="boolean" checked="false"
69 label="Keep only gene with different allele" help="Omit missing" />
70 <param name="duplicate" type="boolean" checked="false"
71 label="Conserve duplicate gene (default remove)" />
72 <param name="inverse" type="boolean" checked="false"
73 label="Keep only gene that not meet the filter of mincover or keep options" />
74 <param name="log" type="boolean" checked="false"
75 label="Write log file" />
76 </inputs>
77 <outputs>
78 <data name="output" format="txt" label="Extract ${export_result.export} on ${database.name}">
79 <change_format>
80 <when input="export_result.export" value="mlst" format="tabular" />
81 <when input="export_result.export" value="distance" format="txt" />
82 <when input="export_result.export" value="strain" format="tabular" />
83 <when input="export_result.export" value="gene" format="txt" />
84 </change_format>
85 </data>
86 <data name="logfile" format="txt" label="${export_result.export} of ${database.name}: log">
87 <filter>log</filter>
88 </data>
89 </outputs>
90 <tests>
91 <test expect_num_outputs="1">
92 <param name="database" value="wgmlst_ecoli.db" />
93 <conditional name="export_result">
94 <param name="export" value="distance" />
95 </conditional>
96 <param name="mincover" value="4" />
97 <output name="output" ftype="txt" file="wgmlst_ecoli.db.distance" />
98 </test>
99 <test expect_num_outputs="1">
100 <param name="database" value="wgmlst_ecoli.db" />
101 <conditional name="export_result">
102 <param name="export" value="mlst" />
103 </conditional>
104 <param name="keep" value="true" />
105 <output name="output" ftype="tabular" file="wgmlst_ecoli.db.mlst" />
106 </test>
107 <test expect_num_outputs="2">
108 <param name="database" value="wgmlst_ecoli.db" />
109 <conditional name="export_result">
110 <param name="export" value="strain" />
111 <param name="count" value="true" />
112 </conditional>
113 <param name="log" value="true" />
114 <output name="output" ftype="tabular" file="wgmlst_ecoli.db.strain" />
115 </test>
116 <test expect_num_outputs="1">
117 <param name="database" value="wgmlst_ecoli.db" />
118 <conditional name="export_result">
119 <param name="export" value="gene" />
120 </conditional>
121 <param name="keep" value="true" />
122 <param name="inverse" value="true" />
123 <output name="output" ftype="txt" file="wgmlst_ecoli.db.gene" />
124 </test>
125 </tests>
126 <help>
127 **What it does**
128
129 Extract element from a cg/wgMLST DATABASE:
130 - an distance matrix
131 - an MLST table
132 - a gene list
133 - an strains list
134
135 Options:
136 -m, --mincover INTEGER Minimun number of strain found to keep a gene
137 (default:0)
138 -k, --keep Keep only gene with different allele (omit missing).
139 -d, --duplicate Conserve duplicate gene (default remove).
140 -V, --inverse Keep only gene that do not meet the filter of
141 mincover or keep options.
142
143 -c, --count Count the number of gene present in the database for
144 each strains.
145
146 **License and citation**
147
148 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
149 </help>
150 <citations>
151 </citations>
152 </tool>