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comparison wade.xml @ 0:92e72350a3c5 draft

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"planemo upload for repository https://github.com/phac-nml/wade commit b3536a15ff4e6295722ec4794ea5b840b5d19276"
author nml
date Fri, 29 Nov 2019 14:57:47 -0500
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children 631e8eb3371e
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-1:000000000000 0:92e72350a3c5
1 <tool id="wade" name="Wade" version="0.2.4+galaxy0">
2 <description>identify regions of interest</description>
3 <requirements>
4 <requirement type="package" version="0.2.4">wade</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7
8 #for $i in $input#
9 cp '$i' '$i.element_identifier' &&
10 #end for
11
12 #set $samples = ','.join([$i.element_identifier for $i in ( $input )])
13
14 Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))'
15
16 -d 'output'
17 -o '$mode.type'
18 -t '$mode.subtype'
19
20 -s '$samples'
21
22 ]]></command>
23 <inputs>
24 <param name="input"
25 type="data" format="fasta"
26 optional="false"
27 multiple="true"
28 label="Contig Fasta file(s)"/>
29 <conditional name="mode">
30 <param name="type" type="select" label="Analysis Group">
31 <option value="GAS">GAS</option>
32 <option value="GONO">GONO</option>
33 <option value="PNEUMO">PNEUMO</option>
34 </param>
35 <when value="GAS">
36 <param name="subtype" type="select" label="Select specific analysis">
37 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
38 <option value="EMM">EMM Typing</option>
39 <option value="MLST">MLST Type</option>
40 <option value="VFDB">VFDB (Virulence Factor Database)</option>
41 <option value="MASTER">Master blaster</option>
42 </param>
43 </when>
44 <when value="GONO">
45 <param name="subtype" type="select" label="Select specific analysis">
46 <option value="MLST">MLST Type</option>
47 <option value="NGMAST">NG-MAST Type</option>
48 <option value="NGSTAR">NG-STAR Type</option>
49 <option value="rRNA23S">23S rRNA Alleles</option>
50 <option value="MASTER">Master blaster</option>
51 </param>
52 </when>
53 <when value="PNEUMO">
54 <param name="subtype" type="select" label="Select specific analysis">
55 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
56 <option value="MLST">MLST Type</option>
57 <option value="VFDB">VFDB (Virulence Factor Database)</option>
58 <option value="rRNA23S">23S rRNA Alleles</option>
59 <option value="MASTER">Master blaster</option>
60 </param>
61 </when>
62 </conditional>
63 </inputs>
64 <outputs>
65 <data name="report" format="csv">
66 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
67 </data>
68 </outputs>
69 <tests>
70 <test>
71 <param name="input" value="SC19-2806-A.fasta"/>
72 <output name='report'>
73 <discovered_dataset designation="GAS_dbpipeline_WADE">
74 <assert_contents>
75 <has_text text="SampleNo" />
76 </assert_contents>
77 </discovered_dataset>
78 </output>
79 </test>
80 </tests>
81 <help><![CDATA[
82 ==============
83 Wade
84 ==============
85
86 R Script to generate results
87
88 =====
89 Legal
90 =====
91
92 Copyright Government of Canada 2019
93
94 Written by: National Microbiology Laboratory, Public Health Agency of Canada
95
96 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
97 this work except in compliance with the License. You may obtain a copy of the
98 License at:
99
100 http://www.apache.org/licenses/LICENSE-2.0
101
102 Unless required by applicable law or agreed to in writing, software distributed
103 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
104 CONDITIONS OF ANY KIND, either express or implied. See the License for the
105 specific language governing permissions and limitations under the License.
106
107 =======
108 Contact
109 =======
110
111 **Gary van Domselaar**: gary.vandomselaar@canada.ca
112
113 ]]></help>
114 <citations>
115 <citation type="bibtex">@ARTICLE{a1,
116 title = {R Script to generate results.},
117 author = {Adrian Zetner},
118 url = {https://github.com/phac-nml/wade}
119 }
120 }</citation>
121 </citations>
122 </tool>