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comparison wgmlst_remove.xml @ 1:5b2c48fa0175 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
author bvalot
date Wed, 07 Dec 2022 15:25:06 +0000
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0:a3cc35af3635 1:5b2c48fa0175
1 <tool id="wgmlst_remove_wrapper"
2 name="Remove strain/gene to cg/wgMLST database"
3 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
4 <description></description>
5 <macros>
6 <import>macro.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <stdio>
10 <exit_code range="1:" level="fatal" />
11 </stdio>
12 <version_command>wgMLST -v</version_command>
13 <command><![CDATA[
14 cp '${database}' '${databaseout}' && wgMLST remove
15 #if $element == "strain"
16 --strains
17 #else
18 --genes
19 #end if
20 #if $data.input == "textinput"
21 '${databaseout}'
22 #for $strain in $data.textelement.split(" ")
23 '$strain'
24 #end for
25 #else
26 -f '${data.fileelement}' '${databaseout}'
27 #end if
28 #if $log
29 2> '${logfile}'
30 #end if
31 ]]>
32 </command>
33 <inputs>
34 <param name="database" type="data"
35 format="sqlite"
36 label="cg/wgMLST database"
37 help="Sqlite format from cg/wgMLST database" />
38 <param name="element" type="select" label="Select type of data to remove">
39 <option value="strain" selected="true">Strain(s)</option>
40 <option value="gene">Gene(s)</option>
41 </param>
42 <conditional name="data">
43 <param name="input" type="select" label="Select source of data">
44 <option value="textinput" selected="true">List elements manually</option>
45 <option value="fileinput">List elements from file</option>
46 </param>
47 <when value="textinput">
48 <param name="textelement" type="text" value="" optional="false" size="50"
49 label="Name of strain/gene to removed from database"
50 help="Separated each strain/gene by a space and quote it"/>
51 </when>
52 <when value="fileinput">
53 <param name="fileelement" type="data" format="txt"
54 label="File list of strain/gene to removed"
55 help="txt format" />
56 </when>
57 </conditional>
58 <param name="log" type="boolean" checked="true"
59 label="Write log file" />
60 </inputs>
61 <outputs>
62 <data name="databaseout" format="sqlite" label="${database.name}">
63 </data>
64 <data name="logfile" format="txt" label="${tool.name} on ${database.name}: log">
65 <filter>log</filter>
66 </data>
67 </outputs>
68 <tests>
69 <test expect_num_outputs="2">
70 <param name="database" value="wgmlst_ecoli.db" />
71 <param name="element" value="strain" />
72 <conditional name="data">
73 <param name="input" value="textinput" />
74 <param name="textelement" value="EEES_003 EEES_004" />
75 </conditional>
76 <output name="logfile" ftype="txt">
77 <assert_contents>
78 <has_text text="EEES_004 : OK" />
79 <has_text text="EEES_003 : OK" />
80 </assert_contents>
81 </output>
82 </test>
83 <test expect_num_outputs="2">
84 <param name="database" value="wgmlst_ecoli.db" />
85 <param name="element" value="gene" />
86 <conditional name="data">
87 <param name="input" value="fileinput" />
88 <param name="fileelement" ftype="txt" value="wgmlst_ecoli.db.gene_to_removed" />
89 </conditional>
90 <output name="logfile" ftype="txt">
91 <assert_contents>
92 <has_text text="b0004 : OK" />
93 <has_text text="C-RS24040 : OK" />
94 <has_text text="ECs4518 : OK" />
95 </assert_contents>
96 </output>
97 </test>
98 </tests>
99 <help>
100 **What it does**
101
102 Remove STRAINS or GENES from a cg/wgMLST DATABASE.
103
104 You can indicated the STRAIN or GENE to remove:
105 - Typing element separated by space
106 - Using a file containing these elements
107
108 **Options:**
109 --strains / --genes Choose the item you wish to remove
110 -f, --file FILENAME File list of genes or strains to removed on the wgMLST database.
111
112 **License and citation**
113
114 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
115 </help>
116 <citations>
117 </citations>
118 </tool>