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annotate 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
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31483f5b6240 "planemo upload for repository https://github.com/phac-nml/wade commit b9586845e0a5e3d53dcfd68459e9b5282bb66549"
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1 <tool id="wade" name="Wade" version="0.2.5+galaxy1">
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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1
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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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631e8eb3371e "planemo upload for repository https://github.com/phac-nml/wade commit 3a5997b52566d197a5103e5a317ce2ed2837065e"
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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
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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 = $mode.subtype_input.subtype
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28 #end if
0
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30 Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))'
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32 -d 'output'
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33
0
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34 -o '$mode.type'
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36 -t '$subtype'
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38 -s '$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">
3
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44 <option value="GAS">Streptococcus pyogenes</option>
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45 <option value="GONO">Streptococcus pneumoniae</option>
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46 <option value="PNEUMO">Neisseria gonorrhoeae</option>
0
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47 </param>
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48 <when value="GAS">
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49 <param name="subtype" type="select" label="Select specific analysis">
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50 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
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51 <option value="EMM">EMM Typing</option>
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52 <option value="MLST">MLST Type</option>
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53 <option value="VFDB">VFDB (Virulence Factor Database)</option>
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54 <option value="MASTER">AMR/Toxin/Virulence Profiler</option>
0
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55 </param>
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56 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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57 </when>
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58 <when value="GONO">
1
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59
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60 <conditional name="subtype_input">
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61 <param name="subtype" type="select" label="Select specific analysis">
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62 <option value="MLST">MLST Type</option>
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63 <option value="NGMAST">NG-MAST Type</option>
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64 <option value="NGSTAR">NG-STAR Type</option>
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65 <option value="rRNA23S">23S rRNA Alleles</option>
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66 <option value="MASTER">AMR/NG-STAR Profiler</option>
0
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67 </param>
1
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68 <when value="rRNA23S">
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69 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
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70 </when>
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71 <when value="MLST">
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72 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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73 </when>
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74 <when value="NGMAST">
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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="NGSTAR">
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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="MASTER">
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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 </conditional>
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84
0
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85 </when>
92e72350a3c5 "planemo upload for repository https://github.com/phac-nml/wade commit b3536a15ff4e6295722ec4794ea5b840b5d19276"
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86 <when value="PNEUMO">
1
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87
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88 <conditional name="subtype_input">
0
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89 <param name="subtype" type="select" label="Select specific analysis">
92e72350a3c5 "planemo upload for repository https://github.com/phac-nml/wade commit b3536a15ff4e6295722ec4794ea5b840b5d19276"
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90 <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
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91 <option value="MLST">MLST Type</option>
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92 <option value="VFDB">VFDB (Virulence Factor Database)</option>
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93 <option value="rRNA23S">23S rRNA Alleles</option>
3
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94 <option value="MASTER">AMR/Virulence Profiler</option>
0
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95 </param>
1
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96 <when value="rRNA23S">
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97 <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
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98 </when>
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99 <when value="AMR">
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100 <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
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101 </when>
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102 <when value="MLST">
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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="VFDB">
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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="MASTER">
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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 </conditional>
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112
0
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113 </when>
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114 </conditional>
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115 </inputs>
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116 <outputs>
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117 <data name="report" format="csv">
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118 <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
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119 </data>
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120 </outputs>
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121 <tests>
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122 <test>
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123 <param name="input" value="SC19-2806-A.fasta"/>
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124 <output name='report'>
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125 <discovered_dataset designation="GAS_dbpipeline_WADE">
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126 <assert_contents>
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127 <has_text text="SampleNo" />
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128 </assert_contents>
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129 </discovered_dataset>
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130 </output>
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 ==============
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135 Wade
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136 ==============
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137
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138 R Script to generate results
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139
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140 =====
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141 Legal
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142 =====
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143
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144 Copyright Government of Canada 2019
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145
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146 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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147
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148 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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149 this work except in compliance with the License. You may obtain a copy of the
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150 License at:
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151
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152 http://www.apache.org/licenses/LICENSE-2.0
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153
92e72350a3c5 "planemo upload for repository https://github.com/phac-nml/wade commit b3536a15ff4e6295722ec4794ea5b840b5d19276"
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154 Unless required by applicable law or agreed to in writing, software distributed
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155 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
92e72350a3c5 "planemo upload for repository https://github.com/phac-nml/wade commit b3536a15ff4e6295722ec4794ea5b840b5d19276"
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156 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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157 specific language governing permissions and limitations under the License.
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158
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159 =======
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160 Contact
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161 =======
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162
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163 **Gary van Domselaar**: gary.vandomselaar@canada.ca
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164
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165 ]]></help>
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166 <citations>
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167 <citation type="bibtex">@ARTICLE{a1,
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168 title = {R Script to generate results.},
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169 author = {Adrian Zetner},
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170 url = {https://github.com/phac-nml/wade}
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171 }
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172 }</citation>
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173 </citations>
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174 </tool>