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comparison wade.xml @ 3:31483f5b6240 draft default tip

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"planemo upload for repository https://github.com/phac-nml/wade commit b9586845e0a5e3d53dcfd68459e9b5282bb66549"
author nml
date Tue, 17 Dec 2019 13:21:08 -0500
parents d1ef975c69f2
children
comparison
equal deleted inserted replaced
2:d1ef975c69f2 3:31483f5b6240
1 <tool id="wade" name="Wade" version="0.2.5+galaxy0"> 1 <tool id="wade" name="Wade" version="0.2.5+galaxy1">
2 <description>identify regions of interest</description> 2 <description>identify regions of interest</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.5">wade</requirement> 4 <requirement type="package" version="0.2.5">wade</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
39 39
40 ]]></command> 40 ]]></command>
41 <inputs> 41 <inputs>
42 <conditional name="mode"> 42 <conditional name="mode">
43 <param name="type" type="select" label="Analysis Group"> 43 <param name="type" type="select" label="Analysis Group">
44 <option value="GAS">GAS</option> 44 <option value="GAS">Streptococcus pyogenes</option>
45 <option value="GONO">GONO</option> 45 <option value="GONO">Streptococcus pneumoniae</option>
46 <option value="PNEUMO">PNEUMO</option> 46 <option value="PNEUMO">Neisseria gonorrhoeae</option>
47 </param> 47 </param>
48 <when value="GAS"> 48 <when value="GAS">
49
50 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
51
52 <param name="subtype" type="select" label="Select specific analysis"> 49 <param name="subtype" type="select" label="Select specific analysis">
53 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option> 50 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
54 <option value="EMM">EMM Typing</option> 51 <option value="EMM">EMM Typing</option>
55 <option value="MLST">MLST Type</option> 52 <option value="MLST">MLST Type</option>
56 <option value="VFDB">VFDB (Virulence Factor Database)</option> 53 <option value="VFDB">VFDB (Virulence Factor Database)</option>
57 <option value="MASTER">Master blaster</option> 54 <option value="MASTER">AMR/Toxin/Virulence Profiler</option>
58 </param> 55 </param>
59 56 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
60 </when> 57 </when>
61 <when value="GONO"> 58 <when value="GONO">
62 59
63 <conditional name="subtype_input"> 60 <conditional name="subtype_input">
64 <param name="subtype" type="select" label="Select specific analysis"> 61 <param name="subtype" type="select" label="Select specific analysis">
65 <option value="MLST">MLST Type</option> 62 <option value="MLST">MLST Type</option>
66 <option value="NGMAST">NG-MAST Type</option> 63 <option value="NGMAST">NG-MAST Type</option>
67 <option value="NGSTAR">NG-STAR Type</option> 64 <option value="NGSTAR">NG-STAR Type</option>
68 <option value="rRNA23S">23S rRNA Alleles</option> 65 <option value="rRNA23S">23S rRNA Alleles</option>
69 <option value="MASTER">Master blaster</option> 66 <option value="MASTER">AMR/NG-STAR Profiler</option>
70 </param> 67 </param>
71 <when value="rRNA23S"> 68 <when value="rRNA23S">
72 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/> 69 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
73 </when> 70 </when>
74 <when value="MLST"> 71 <when value="MLST">
92 <param name="subtype" type="select" label="Select specific analysis"> 89 <param name="subtype" type="select" label="Select specific analysis">
93 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option> 90 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
94 <option value="MLST">MLST Type</option> 91 <option value="MLST">MLST Type</option>
95 <option value="VFDB">VFDB (Virulence Factor Database)</option> 92 <option value="VFDB">VFDB (Virulence Factor Database)</option>
96 <option value="rRNA23S">23S rRNA Alleles</option> 93 <option value="rRNA23S">23S rRNA Alleles</option>
97 <option value="MASTER">Master blaster</option> 94 <option value="MASTER">AMR/Virulence Profiler</option>
98 </param> 95 </param>
99 <when value="rRNA23S"> 96 <when value="rRNA23S">
100 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/> 97 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
101 </when> 98 </when>
102 <when value="AMR"> 99 <when value="AMR">