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annotate wade.xml @ 2:d1ef975c69f2 draft

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"planemo upload for repository https://github.com/phac-nml/wade commit d78afd73dbdf5b292bc8fe210523dda44c5cb86d"
author nml
date Thu, 05 Dec 2019 11:34:17 -0500
parents 631e8eb3371e
children 31483f5b6240
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2
d1ef975c69f2 "planemo upload for repository https://github.com/phac-nml/wade commit d78afd73dbdf5b292bc8fe210523dda44c5cb86d"
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1 <tool id="wade" name="Wade" version="0.2.5+galaxy0">
0
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2 <description>identify regions of interest</description>
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3 <requirements>
2
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4 <requirement type="package" version="0.2.5">wade</requirement>
0
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7
1
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9
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10 #if $mode.type == 'GAS':
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12 #for $i in $mode.input#
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13 cp '$i' '$i.element_identifier' &&
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14 #end for
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15
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16 #set $samples = ','.join([$i.element_identifier for $i in ( $mode.input )])
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17 #set $subtype = $mode.subtype
0
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18
1
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19 #else:
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21 #for $i in $mode.subtype_input.input#
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22 cp '$i' '$i.element_identifier' &&
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23 #end for
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25 #set $samples = ','.join([$i.element_identifier for $i in ( $mode.subtype_input.input )])
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26 #set $subtype = $mode.subtype_input.subtype
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28 #end if
0
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29
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30 Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))'
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32 -d 'output'
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33
0
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34 -o '$mode.type'
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631e8eb3371e "planemo upload for repository https://github.com/phac-nml/wade commit 3a5997b52566d197a5103e5a317ce2ed2837065e"
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36 -t '$subtype'
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37
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38 -s '$samples'
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39
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40 ]]></command>
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41 <inputs>
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42 <conditional name="mode">
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43 <param name="type" type="select" label="Analysis Group">
92e72350a3c5 "planemo upload for repository https://github.com/phac-nml/wade commit b3536a15ff4e6295722ec4794ea5b840b5d19276"
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44 <option value="GAS">GAS</option>
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45 <option value="GONO">GONO</option>
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46 <option value="PNEUMO">PNEUMO</option>
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47 </param>
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48 <when value="GAS">
1
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49
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50 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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51
0
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52 <param name="subtype" type="select" label="Select specific analysis">
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53 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
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54 <option value="EMM">EMM Typing</option>
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55 <option value="MLST">MLST Type</option>
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56 <option value="VFDB">VFDB (Virulence Factor Database)</option>
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57 <option value="MASTER">Master blaster</option>
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58 </param>
1
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59
0
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60 </when>
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61 <when value="GONO">
1
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63 <conditional name="subtype_input">
0
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64 <param name="subtype" type="select" label="Select specific analysis">
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65 <option value="MLST">MLST Type</option>
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66 <option value="NGMAST">NG-MAST Type</option>
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67 <option value="NGSTAR">NG-STAR Type</option>
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68 <option value="rRNA23S">23S rRNA Alleles</option>
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69 <option value="MASTER">Master blaster</option>
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70 </param>
1
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71 <when value="rRNA23S">
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72 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
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73 </when>
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74 <when value="MLST">
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75 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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76 </when>
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77 <when value="NGMAST">
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78 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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79 </when>
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80 <when value="NGSTAR">
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81 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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82 </when>
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83 <when value="MASTER">
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84 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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85 </when>
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86 </conditional>
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87
0
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88 </when>
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89 <when value="PNEUMO">
1
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90
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91 <conditional name="subtype_input">
0
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92 <param name="subtype" type="select" label="Select specific analysis">
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93 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
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94 <option value="MLST">MLST Type</option>
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95 <option value="VFDB">VFDB (Virulence Factor Database)</option>
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96 <option value="rRNA23S">23S rRNA Alleles</option>
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97 <option value="MASTER">Master blaster</option>
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98 </param>
1
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99 <when value="rRNA23S">
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100 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
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101 </when>
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102 <when value="AMR">
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103 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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104 </when>
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105 <when value="MLST">
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106 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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107 </when>
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108 <when value="VFDB">
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109 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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110 </when>
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111 <when value="MASTER">
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112 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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113 </when>
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114 </conditional>
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115
0
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116 </when>
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117 </conditional>
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118 </inputs>
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119 <outputs>
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120 <data name="report" format="csv">
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121 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
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122 </data>
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123 </outputs>
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124 <tests>
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125 <test>
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126 <param name="input" value="SC19-2806-A.fasta"/>
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127 <output name='report'>
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128 <discovered_dataset designation="GAS_dbpipeline_WADE">
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129 <assert_contents>
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130 <has_text text="SampleNo" />
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131 </assert_contents>
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132 </discovered_dataset>
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133 </output>
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134 </test>
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135 </tests>
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136 <help><![CDATA[
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137 ==============
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138 Wade
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139 ==============
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140
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141 R Script to generate results
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142
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143 =====
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144 Legal
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145 =====
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146
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147 Copyright Government of Canada 2019
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148
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149 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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150
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151 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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152 this work except in compliance with the License. You may obtain a copy of the
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153 License at:
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154
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155 http://www.apache.org/licenses/LICENSE-2.0
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156
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157 Unless required by applicable law or agreed to in writing, software distributed
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158 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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159 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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160 specific language governing permissions and limitations under the License.
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161
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162 =======
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163 Contact
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164 =======
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165
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166 **Gary van Domselaar**: gary.vandomselaar@canada.ca
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167
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168 ]]></help>
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169 <citations>
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170 <citation type="bibtex">@ARTICLE{a1,
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171 title = {R Script to generate results.},
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172 author = {Adrian Zetner},
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173 url = {https://github.com/phac-nml/wade}
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174 }
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175 }</citation>
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176 </citations>
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177 </tool>