Mercurial > repos > nml > wade
comparison wade.xml @ 3:31483f5b6240 draft default tip
"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 |
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| 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"> |