Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_tools_import.xml @ 4:914fa4daf16a draft
Fixes
| author | florianbegusch |
|---|---|
| date | Wed, 31 Jul 2019 03:06:00 -0400 |
| parents | 370e0b6e9826 |
| children | f190567fe3f6 |
comparison
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| 3:558645416841 | 4:914fa4daf16a |
|---|---|
| 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> |