Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_tools_import.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
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3:eda5df31da55 4:71f124e02000
42 #else 42 #else
43 #set $file_for_processing = "'input/" + $f.name + "'" 43 #set $file_for_processing = "'input/" + $f.name + "'"
44 ln -s ${f} $file_for_processing; 44 ln -s ${f} $file_for_processing;
45 #end if 45 #end if
46 #end for 46 #end for
47 #if 'SingleEndFastqManifestPhred' in str($sourceformat): 47 #if 'SingleEndFastqManifestPhred' in str($inputformat):
48 #set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt" 48 #set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt"
49 #set $m_file = open(str($cwd), 'w') 49 #set $m_file = open(str($cwd), 'w')
50 $m_file.write("sample-id,absolute-filepath,direction\n") 50 $m_file.write("sample-id,absolute-filepath,direction\n")
51 #for $f in $input_type.list_list: 51 #for $f in $input_type.list_list:
52 $m_file.write(str($f.name).split("_")[0]+",$PWD/input/"+str($f.name)+".gz,forward\n") 52 $m_file.write(str($f.name).split("_")[0]+",$PWD/input/"+str($f.name)+".gz,forward\n")
83 #end if 83 #end if
84 #end for 84 #end for
85 85
86 86
87 $m_file.close() 87 $m_file.close()
88 #if 'PairedEndFastqManifestPhred' in str($sourceformat): 88 #if 'PairedEndFastqManifestPhred' in str($inputformat):
89 #set $in_= str($cwd) 89 #set $in_= str($cwd)
90 #elif 'Casava' in str($sourceformat): 90 #elif 'Casava' in str($inputformat):
91 #set $in_= 'input' 91 #set $in_= 'input'
92 #end if 92 #end if
93 93
94 #else 94 #else
95 #set $res = $is_fastq(str($file)) 95 #set $res = $is_fastq(str($file))
117 #end if 117 #end if
118 118
119 119
120 qiime tools import 120 qiime tools import
121 121
122 --input-path=$in_
123
124 #if str($inputformat) != 'None':
125 #if '__ob__' in str($inputformat):
126 #set $inputformat_temp = str($inputformat).replace('__ob__', '[')
127 #set $inputformat_temp = str($inputformat_temp).replace('__cb__', ']')
128 #set $inputformat = $inputformat_temp
129 #end if
130 --input-format="$inputformat"
131 #end if
132
122 --type="$semantic_type" 133 --type="$semantic_type"
123 134
124 --input-path=$in_
125
126 --output-path=outputpath.qza 135 --output-path=outputpath.qza
127 136
128 #if str($sourceformat) != 'None':
129 #if '__ob__' in str($sourceformat):
130 #set $sourceformat_temp = str($sourceformat).replace('__ob__', '[')
131 #set $sourceformat_temp = str($sourceformat_temp).replace('__cb__', ']')
132 #set $sourceformat = $sourceformat_temp
133 #end if
134 --source-format="$sourceformat"
135 #end if
136 ; 137 ;
137 cp outputpath.qza $outputpath 138 cp outputpath.qza $outputpath
138 ]]> 139 ]]>
139 </command> 140 </command>
140 <inputs> 141 <inputs>
159 <param label="--type: The semantic type of the artifact that will be created upon importing. [required]" name="semantic_type" optional="False" type="select"> 160 <param label="--type: The semantic type of the artifact that will be created upon importing. [required]" name="semantic_type" optional="False" type="select">
160 <option value="DeblurStats">DeblurStats</option> 161 <option value="DeblurStats">DeblurStats</option>
161 <option value="DistanceMatrix">DistanceMatrix</option> 162 <option value="DistanceMatrix">DistanceMatrix</option>
162 <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> 163 <option value="EMPPairedEndSequences">EMPPairedEndSequences</option>
163 <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> 164 <option value="EMPSingleEndSequences">EMPSingleEndSequences</option>
165 <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option>
164 <option value="FeatureData[AlignedSequence]">FeatureData[AlignedSequence]</option> 166 <option value="FeatureData[AlignedSequence]">FeatureData[AlignedSequence]</option>
167 <option value="FeatureData[Importance]">FeatureData[Importance]</option>
165 <option value="FeatureData[PairedEndSequence]">FeatureData[PairedEndSequence]</option> 168 <option value="FeatureData[PairedEndSequence]">FeatureData[PairedEndSequence]</option>
166 <option value="FeatureData[Sequence]">FeatureData[Sequence]</option> 169 <option value="FeatureData[Sequence]">FeatureData[Sequence]</option>
167 <option value="FeatureData[Taxonomy]">FeatureData[Taxonomy]</option> 170 <option value="FeatureData[Taxonomy]">FeatureData[Taxonomy]</option>
168 <option value="FeatureTable[Balance]">FeatureTable[Balance]</option> 171 <option value="FeatureTable[Balance]">FeatureTable[Balance]</option>
169 <option value="FeatureTable[Composition]">FeatureTable[Composition]</option> 172 <option value="FeatureTable[Composition]">FeatureTable[Composition]</option>
170 <option value="FeatureTable[Frequency]">FeatureTable[Frequency]</option> 173 <option value="FeatureTable[Frequency]">FeatureTable[Frequency]</option>
174 <option value="FeatureTable[PercentileNormalized]">FeatureTable[PercentileNormalized]</option>
171 <option value="FeatureTable[PresenceAbsence]">FeatureTable[PresenceAbsence]</option> 175 <option value="FeatureTable[PresenceAbsence]">FeatureTable[PresenceAbsence]</option>
172 <option value="FeatureTable[RelativeFrequency]">FeatureTable[RelativeFrequency]</option> 176 <option value="FeatureTable[RelativeFrequency]">FeatureTable[RelativeFrequency]</option>
173 <option value="Hierarchy">Hierarchy</option> 177 <option value="Hierarchy">Hierarchy</option>
174 <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> 178 <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>
175 <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> 179 <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option>
176 <option value="PCoAResults">PCoAResults</option> 180 <option value="PCoAResults">PCoAResults</option>
177 <option value="Phylogeny[Rooted]">Phylogeny[Rooted]</option> 181 <option value="Phylogeny[Rooted]">Phylogeny[Rooted]</option>
178 <option value="Phylogeny[Unrooted]">Phylogeny[Unrooted]</option> 182 <option value="Phylogeny[Unrooted]">Phylogeny[Unrooted]</option>
183 <option value="Placements">Placements</option>
179 <option value="QualityFilterStats">QualityFilterStats</option> 184 <option value="QualityFilterStats">QualityFilterStats</option>
180 <option value="RawSequences">RawSequences</option> 185 <option value="RawSequences">RawSequences</option>
181 <option value="SampleData[AlphaDiversity]">SampleData[AlphaDiversity]</option> 186 <option value="SampleData[AlphaDiversity]">SampleData[AlphaDiversity]</option>
182 <option value="SampleData[BooleanSeries]">SampleData[BooleanSeries]</option> 187 <option value="SampleData[BooleanSeries]">SampleData[BooleanSeries]</option>
188 <option value="SampleData[ClassifierPredictions]">SampleData[ClassifierPredictions]</option>
183 <option value="SampleData[DADA2Stats]">SampleData[DADA2Stats]</option> 189 <option value="SampleData[DADA2Stats]">SampleData[DADA2Stats]</option>
184 <option value="SampleData[FirstDifferences]">SampleData[FirstDifferences]</option> 190 <option value="SampleData[FirstDifferences]">SampleData[FirstDifferences]</option>
185 <option value="SampleData[JoinedSequencesWithQuality]">SampleData[JoinedSequencesWithQuality]</option> 191 <option value="SampleData[JoinedSequencesWithQuality]">SampleData[JoinedSequencesWithQuality]</option>
186 <option selected="True" value="SampleData[PairedEndSequencesWithQuality]">SampleData[PairedEndSequencesWithQuality]</option> 192 <option selected="True" value="SampleData[PairedEndSequencesWithQuality]">SampleData[PairedEndSequencesWithQuality]</option>
193 <option value="SampleData[RegressorPredictions]">SampleData[RegressorPredictions]</option>
187 <option value="SampleData[SequencesWithQuality]">SampleData[SequencesWithQuality]</option> 194 <option value="SampleData[SequencesWithQuality]">SampleData[SequencesWithQuality]</option>
188 <option value="SampleData[Sequences]">SampleData[Sequences]</option> 195 <option value="SampleData[Sequences]">SampleData[Sequences]</option>
196 <option value="SampleData[Classifier]">SampleData[Classifier]</option>
197 <option value="SampleData[Regressor]">SampleData[Regressor]</option>
189 <option value="TaxonomicClassifier">TaxonomicClassifier</option> 198 <option value="TaxonomicClassifier">TaxonomicClassifier</option>
190 <option value="UchimeStats">UchimeStats</option> 199 <option value="UchimeStats">UchimeStats</option>
191 </param> 200 </param>
192 201
193 <param label="--source-format: The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type." name="sourceformat" optional="True" type="select"> 202 <param label="--input-format: The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type." name="inputformat" optional="True" type="select">
194 <option value="AlignedDNAFASTAFormat">AlignedDNAFASTAFormat</option> 203 <option value="AlignedDNAFASTAFormat">AlignedDNAFASTAFormat</option>
195 <option value="AlignedDNASequencesDirectoryFormat">AlignedDNASequencesDirectoryFormat</option> 204 <option value="AlignedDNASequencesDirectoryFormat">AlignedDNASequencesDirectoryFormat</option>
196 <option value="AlphaDiversityDirectoryFormat">AlphaDiversityDirectoryFormat</option> 205 <option value="AlphaDiversityDirectoryFormat">AlphaDiversityDirectoryFormat</option>
197 <option value="AlphaDiversityFormat">AlphaDiversityFormat</option> 206 <option value="AlphaDiversityFormat">AlphaDiversityFormat</option>
198 <option value="BIOMV100DirFmt">BIOMV100DirFmt</option> 207 <option value="BIOMV100DirFmt">BIOMV100DirFmt</option>
212 <option value="DistanceMatrixDirectoryFormat">DistanceMatrixDirectoryFormat</option> 221 <option value="DistanceMatrixDirectoryFormat">DistanceMatrixDirectoryFormat</option>
213 <option value="EMPPairedEndCasavaDirFmt">EMPPairedEndCasavaDirFmt</option> 222 <option value="EMPPairedEndCasavaDirFmt">EMPPairedEndCasavaDirFmt</option>
214 <option value="EMPPairedEndDirFmt">EMPPairedEndDirFmt</option> 223 <option value="EMPPairedEndDirFmt">EMPPairedEndDirFmt</option>
215 <option value="EMPSingleEndCasavaDirFmt">EMPSingleEndCasavaDirFmt</option> 224 <option value="EMPSingleEndCasavaDirFmt">EMPSingleEndCasavaDirFmt</option>
216 <option value="EMPSingleEndDirFmt">EMPSingleEndDirFmt</option> 225 <option value="EMPSingleEndDirFmt">EMPSingleEndDirFmt</option>
226 <option value="ErrorCorrectionDetailsDirFmt">ErrorCorrectionDetailsDirFmt</option>
217 <option value="FastqGzFormat">FastqGzFormat</option> 227 <option value="FastqGzFormat">FastqGzFormat</option>
218 <option value="FirstDifferencesDirectoryFormat">FirstDifferencesDirectoryFormat</option> 228 <option value="FirstDifferencesDirectoryFormat">FirstDifferencesDirectoryFormat</option>
219 <option value="FirstDifferencesFormat">FirstDifferencesFormat</option> 229 <option value="FirstDifferencesFormat">FirstDifferencesFormat</option>
220 <option value="HeaderlessTSVTaxonomyDirectoryFormat">HeaderlessTSVTaxonomyDirectoryFormat</option> 230 <option value="HeaderlessTSVTaxonomyDirectoryFormat">HeaderlessTSVTaxonomyDirectoryFormat</option>
221 <option value="HeaderlessTSVTaxonomyFormat">HeaderlessTSVTaxonomyFormat</option> 231 <option value="HeaderlessTSVTaxonomyFormat">HeaderlessTSVTaxonomyFormat</option>
232 <option value="ImportanceDirectoryFormat">ImportanceDirectoryFormat</option>
233 <option value="ImportanceFormat">ImportanceFormat</option>
222 <option value="LSMatFormat">LSMatFormat</option> 234 <option value="LSMatFormat">LSMatFormat</option>
223 <option value="MultiplexedPairedEndBarcodeInSequenceDirFmt">MultiplexedPairedEndBarcodeInSequenceDirFmt</option> 235 <option value="MultiplexedPairedEndBarcodeInSequenceDirFmt">MultiplexedPairedEndBarcodeInSequenceDirFmt</option>
224 <option value="MultiplexedSingleEndBarcodeInSequenceDirFmt">MultiplexedSingleEndBarcodeInSequenceDirFmt</option> 236 <option value="MultiplexedSingleEndBarcodeInSequenceDirFmt">MultiplexedSingleEndBarcodeInSequenceDirFmt</option>
225 <option value="NewickDirectoryFormat">NewickDirectoryFormat</option> 237 <option value="NewickDirectoryFormat">NewickDirectoryFormat</option>
226 <option value="NewickFormat">NewickFormat</option> 238 <option value="NewickFormat">NewickFormat</option>
227 <option value="OrdinationDirectoryFormat">OrdinationDirectoryFormat</option> 239 <option value="OrdinationDirectoryFormat">OrdinationDirectoryFormat</option>
228 <option value="OrdinationFormat">OrdinationFormat</option> 240 <option value="OrdinationFormat">OrdinationFormat</option>
229 <option value="PairedDNASequencesDirectoryFormat">PairedDNASequencesDirectoryFormat</option> 241 <option value="PairedDNASequencesDirectoryFormat">PairedDNASequencesDirectoryFormat</option>
230 <option selected="True" value="PairedEndFastqManifestPhred33">PairedEndFastqManifestPhred33</option> 242 <option value="PairedEndFastqManifestPhred33">PairedEndFastqManifestPhred33</option>
243 <option value="PairedEndFastqManifestPhred33V2">PairedEndFastqManifestPhred33V2</option>
231 <option value="PairedEndFastqManifestPhred64">PairedEndFastqManifestPhred64</option> 244 <option value="PairedEndFastqManifestPhred64">PairedEndFastqManifestPhred64</option>
245 <option value="PairedEndFastqManifestPhred64V2">PairedEndFastqManifestPhred64V2</option>
246 <option value="PlacementsDirFmt">PlacementsDirFmt</option>
247 <option value="PlacementsFormat">PlacementsFormat</option>
248 <option value="PredictionsDirectoryFormat">PredictionsDirectoryFormat</option>
249 <option value="PredictionsFormat">PredictionsFormat</option>
232 <option value="QIIME1DemuxDirFmt">QIIME1DemuxDirFmt</option> 250 <option value="QIIME1DemuxDirFmt">QIIME1DemuxDirFmt</option>
233 <option value="QIIME1DemuxFormat">QIIME1DemuxFormat</option> 251 <option value="QIIME1DemuxFormat">QIIME1DemuxFormat</option>
234 <option value="QualityFilterStatsDirFmt">QualityFilterStatsDirFmt</option> 252 <option value="QualityFilterStatsDirFmt">QualityFilterStatsDirFmt</option>
235 <option value="QualityFilterStatsFmt">QualityFilterStatsFmt</option> 253 <option value="QualityFilterStatsFmt">QualityFilterStatsFmt</option>
254 <option value="SampleEstimatorDirFmt">SampleEstimatorDirFmt</option>
236 <option value="SingleEndFastqManifestPhred33">SingleEndFastqManifestPhred33</option> 255 <option value="SingleEndFastqManifestPhred33">SingleEndFastqManifestPhred33</option>
256 <option value="SingleEndFastqManifestPhred33V2">SingleEndFastqManifestPhred33V2</option>
237 <option value="SingleEndFastqManifestPhred64">SingleEndFastqManifestPhred64</option> 257 <option value="SingleEndFastqManifestPhred64">SingleEndFastqManifestPhred64</option>
258 <option value="SingleEndFastqManifestPhred64V2">SingleEndFastqManifestPhred64V2</option>
238 <option value="SingleLanePerSamplePairedEndFastqDirFmt">SingleLanePerSamplePairedEndFastqDirFmt</option> 259 <option value="SingleLanePerSamplePairedEndFastqDirFmt">SingleLanePerSamplePairedEndFastqDirFmt</option>
239 <option value="SingleLanePerSampleSingleEndFastqDirFmt">SingleLanePerSampleSingleEndFastqDirFmt</option> 260 <option value="SingleLanePerSampleSingleEndFastqDirFmt">SingleLanePerSampleSingleEndFastqDirFmt</option>
240 <option value="TSVTaxonomyDirectoryFormat">TSVTaxonomyDirectoryFormat</option> 261 <option value="TSVTaxonomyDirectoryFormat">TSVTaxonomyDirectoryFormat</option>
241 <option value="TSVTaxonomyFormat">TSVTaxonomyFormat</option> 262 <option value="TSVTaxonomyFormat">TSVTaxonomyFormat</option>
242 <option value="TaxonomicClassiferTemporaryPickleDirFmt">TaxonomicClassiferTemporaryPickleDirFmt</option> 263 <option value="TaxonomicClassiferTemporaryPickleDirFmt">TaxonomicClassiferTemporaryPickleDirFmt</option>