Mercurial > repos > nml > wade
comparison wade.xml @ 1:631e8eb3371e draft
"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 |
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| 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"> |