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comparison wade.xml @ 1:631e8eb3371e draft

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"planemo upload for repository https://github.com/phac-nml/wade commit 3a5997b52566d197a5103e5a317ce2ed2837065e"
author nml
date Tue, 03 Dec 2019 12:08:14 -0500
parents 92e72350a3c5
children d1ef975c69f2
comparison
equal deleted inserted replaced
0:92e72350a3c5 1:631e8eb3371e
1 <tool id="wade" name="Wade" version="0.2.4+galaxy0"> 1 <tool id="wade" name="Wade" version="0.2.4+galaxy1">
2 <description>identify regions of interest</description> 2 <description>identify regions of interest</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.4">wade</requirement> 4 <requirement type="package" version="0.2.4">wade</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 #for $i in $input#
9 cp '$i' '$i.element_identifier' &&
10 #end for
11 8
12 #set $samples = ','.join([$i.element_identifier for $i in ( $input )]) 9
10 #if $mode.type == 'GAS':
11
12 #for $i in $mode.input#
13 cp '$i' '$i.element_identifier' &&
14 #end for
15
16 #set $samples = ','.join([$i.element_identifier for $i in ( $mode.input )])
17 #set $subtype = $mode.subtype
18
19 #else:
20
21 #for $i in $mode.subtype_input.input#
22 cp '$i' '$i.element_identifier' &&
23 #end for
24
25 #set $samples = ','.join([$i.element_identifier for $i in ( $mode.subtype_input.input )])
26 #set $subtype = $mode.subtype_input.subtype
27
28 #end if
13 29
14 Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))' 30 Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))'
15 31
16 -d 'output' 32 -d 'output'
33
17 -o '$mode.type' 34 -o '$mode.type'
18 -t '$mode.subtype' 35
36 -t '$subtype'
19 37
20 -s '$samples' 38 -s '$samples'
21 39
22 ]]></command> 40 ]]></command>
23 <inputs> 41 <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"> 42 <conditional name="mode">
30 <param name="type" type="select" label="Analysis Group"> 43 <param name="type" type="select" label="Analysis Group">
31 <option value="GAS">GAS</option> 44 <option value="GAS">GAS</option>
32 <option value="GONO">GONO</option> 45 <option value="GONO">GONO</option>
33 <option value="PNEUMO">PNEUMO</option> 46 <option value="PNEUMO">PNEUMO</option>
34 </param> 47 </param>
35 <when value="GAS"> 48 <when value="GAS">
49
50 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
51
36 <param name="subtype" type="select" label="Select specific analysis"> 52 <param name="subtype" type="select" label="Select specific analysis">
37 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option> 53 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
38 <option value="EMM">EMM Typing</option> 54 <option value="EMM">EMM Typing</option>
39 <option value="MLST">MLST Type</option> 55 <option value="MLST">MLST Type</option>
40 <option value="VFDB">VFDB (Virulence Factor Database)</option> 56 <option value="VFDB">VFDB (Virulence Factor Database)</option>
41 <option value="MASTER">Master blaster</option> 57 <option value="MASTER">Master blaster</option>
42 </param> 58 </param>
59
43 </when> 60 </when>
44 <when value="GONO"> 61 <when value="GONO">
62
63 <conditional name="subtype_input">
45 <param name="subtype" type="select" label="Select specific analysis"> 64 <param name="subtype" type="select" label="Select specific analysis">
46 <option value="MLST">MLST Type</option> 65 <option value="MLST">MLST Type</option>
47 <option value="NGMAST">NG-MAST Type</option> 66 <option value="NGMAST">NG-MAST Type</option>
48 <option value="NGSTAR">NG-STAR Type</option> 67 <option value="NGSTAR">NG-STAR Type</option>
49 <option value="rRNA23S">23S rRNA Alleles</option> 68 <option value="rRNA23S">23S rRNA Alleles</option>
50 <option value="MASTER">Master blaster</option> 69 <option value="MASTER">Master blaster</option>
51 </param> 70 </param>
71 <when value="rRNA23S">
72 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
73 </when>
74 <when value="MLST">
75 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
76 </when>
77 <when value="NGMAST">
78 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
79 </when>
80 <when value="NGSTAR">
81 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
82 </when>
83 <when value="MASTER">
84 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
85 </when>
86 </conditional>
87
52 </when> 88 </when>
53 <when value="PNEUMO"> 89 <when value="PNEUMO">
90
91 <conditional name="subtype_input">
54 <param name="subtype" type="select" label="Select specific analysis"> 92 <param name="subtype" type="select" label="Select specific analysis">
55 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option> 93 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
56 <option value="MLST">MLST Type</option> 94 <option value="MLST">MLST Type</option>
57 <option value="VFDB">VFDB (Virulence Factor Database)</option> 95 <option value="VFDB">VFDB (Virulence Factor Database)</option>
58 <option value="rRNA23S">23S rRNA Alleles</option> 96 <option value="rRNA23S">23S rRNA Alleles</option>
59 <option value="MASTER">Master blaster</option> 97 <option value="MASTER">Master blaster</option>
60 </param> 98 </param>
99 <when value="rRNA23S">
100 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
101 </when>
102 <when value="AMR">
103 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
104 </when>
105 <when value="MLST">
106 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
107 </when>
108 <when value="VFDB">
109 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
110 </when>
111 <when value="MASTER">
112 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
113 </when>
114 </conditional>
115
61 </when> 116 </when>
62 </conditional> 117 </conditional>
63 </inputs> 118 </inputs>
64 <outputs> 119 <outputs>
65 <data name="report" format="csv"> 120 <data name="report" format="csv">