Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_tools_import.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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28:c28331a63dfd | 29:3ba9833030c1 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_tools_import" name="qiime tools import" version="2020.8"> | |
3 <description> - Import data into a new QIIME 2 Artifact.</description> | |
4 <requirements> | |
5 <requirement type="package" version="2020.8">qiime2</requirement> | |
6 </requirements> | |
7 <command> | |
8 <![CDATA[ | |
9 mkdir input; | |
10 | |
11 #set $in_= 'input' | |
12 | |
13 | |
14 #if '__ob__' in str($semantic_type): | |
15 #set $type_temp = str($semantic_type).replace('__ob__', '[') | |
16 #set $type_temp = str($type_temp).replace('__cb__', ']') | |
17 #set $semantic_type = $type_temp | |
18 #end if | |
19 | |
20 #def is_fastq($f_test) | |
21 #set $f = open($f_test, 'rb') | |
22 #set $fastq = str($f.readline()[0]) | |
23 #if str($f.readline()[0]) == '@' | |
24 #$f.close() | |
25 #return True | |
26 #end if | |
27 | |
28 #$f.close() | |
29 #return $fastq | |
30 #end def | |
31 | |
32 | |
33 ## Symlinks creation or On the fly creation of a combo file | |
34 #if $input_type.type == 'list_list' | |
35 ## Symlinks creation or On the fly creation of a combo file | |
36 #for $f in $input_type.list_list: | |
37 | |
38 #set $is_fastq_file = $is_fastq(str($f)) | |
39 | |
40 #if $is_fastq_file: | |
41 #set $file_for_processing = "'input/" + $f.name + '.gz' + "'" | |
42 gzip -c ${f} > $file_for_processing; | |
43 ##echo $is_fastq_file; | |
44 #else | |
45 #set $file_for_processing = "'input/" + $f.name + "'" | |
46 ln -s ${f} $file_for_processing; | |
47 ##echo $is_fastq_file; | |
48 #end if | |
49 #end for | |
50 #if 'SingleEndFastqManifestPhred' in str($inputformat): | |
51 #set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt" | |
52 #set $tt = str("sample-id,absolute-filepath,direction") | |
53 echo $tt >> $cwf; | |
54 #for $f in $input_type.list_list: | |
55 #set $tt = str($f.name).split("_")[0]+",$PWD/input/"+str($f.name).split(".")[0]+".fastq.gz,forward\n" | |
56 echo $tt >> $cwf; | |
57 #end for | |
58 | |
59 #set $in_= str($cwf) | |
60 #end if | |
61 | |
62 | |
63 #elif $input_type.type == 'list_paired_collection': | |
64 | |
65 #set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt" | |
66 #set $tt = str("sample-id,absolute-filepath,direction") | |
67 echo $tt >> $cwf; | |
68 | |
69 #for $pair in $input_type.list_paired_collection: | |
70 #set $forward_is_fastq_file = $is_fastq(str($pair.forward)) | |
71 #set $reverse_is_fastq_file = $is_fastq(str($pair.reverse)) | |
72 | |
73 #if $forward_is_fastq_file: | |
74 gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz; | |
75 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n" | |
76 echo $tt >> $cwf; | |
77 #else | |
78 ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz; | |
79 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n" | |
80 echo $tt >> $cwf; | |
81 #end if | |
82 | |
83 #if $reverse_is_fastq_file: | |
84 gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz; | |
85 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n" | |
86 echo $tt >> $cwf; | |
87 #else | |
88 ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz; | |
89 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n" | |
90 echo $tt >> $cwf; | |
91 #end if | |
92 #end for | |
93 | |
94 | |
95 | |
96 #if 'PairedEndFastqManifestPhred' in str($inputformat) or 'SingleEndFastqManifestPhred33V2' in str($inputformat) or 'SingleEndFastqManifestPhred33' in str($inputformat): | |
97 | |
98 #set $in_= str($cwf) | |
99 | |
100 #elif 'Casava' in str($inputformat): | |
101 #set $in_= 'input' | |
102 #end if | |
103 | |
104 | |
105 #else | |
106 #set $res = $is_fastq(str($file)) | |
107 | |
108 #if $res | |
109 gzip -c ${file} > ${file.name}.gz; | |
110 #set $in_= $file.name + '.gz' | |
111 | |
112 #else | |
113 #set $in_= str($file) | |
114 #end if | |
115 | |
116 #if "MultiplexedSingleEndBarcodeInSequence" in str($semantic_type): | |
117 mv *_R1_* forward.fastq.gz; | |
118 #set $in_= 'forward.fastq.gz'; | |
119 #end if | |
120 | |
121 #end if | |
122 | |
123 | |
124 ## rename files to predefined names for "MultiplexedPairedEndBarcodeInSequence" | |
125 #if "MultiplexedPairedEndBarcodeInSequence" in str($semantic_type): | |
126 mv input/*_R1_* input/forward.fastq.gz; | |
127 mv input/*_R2_* input/reverse.fastq.gz; | |
128 #end if | |
129 | |
130 | |
131 qiime tools import | |
132 | |
133 --input-path=$in_ | |
134 | |
135 #if str($inputformat) != 'None': | |
136 #if '__ob__' in str($inputformat): | |
137 #set $inputformat_temp = str($inputformat).replace('__ob__', '[') | |
138 #set $inputformat_temp = str($inputformat_temp).replace('__cb__', ']') | |
139 #set $inputformat = $inputformat_temp | |
140 #end if | |
141 --input-format="$inputformat" | |
142 #end if | |
143 | |
144 --type="$semantic_type" | |
145 | |
146 --output-path=outputpath.qza | |
147 | |
148 ; | |
149 cp outputpath.qza $outputpath | |
150 ]]> | |
151 </command> | |
152 <inputs> | |
153 <conditional name="input_type"> | |
154 <param name="type" type="select" label="Select a way to provide data, either using a file or a list" help=""> | |
155 <option value="regular">Input file</option> | |
156 <option selected="true" value="list_paired_collection">Multiple pairs - Combo mode (list:paired collection)</option> | |
157 <option value="list_list">Input list</option> | |
158 </param> | |
159 | |
160 <when value="regular"> | |
161 <param name="file" type="data" multiple="false" label="Input file" /> | |
162 </when> | |
163 <when value="list_paired_collection"> | |
164 <param name="list_paired_collection" type="data_collection" collection_type="list:paired" label="Fastq pairs (collection)" help="Dataset collection made from multiple pairs of files" /> | |
165 </when> | |
166 <when value="list_list"> | |
167 <param name="list_list" type="data_collection" collection_type="list" label="Input list" /> | |
168 </when> | |
169 </conditional> | |
170 | |
171 <param label="--type: The semantic type of the artifact that will be created upon importing. [required]" name="semantic_type" optional="False" type="select"> | |
172 <option value="DeblurStats">DeblurStats</option> | |
173 <option value="DistanceMatrix">DistanceMatrix</option> | |
174 <option value="EMPPairedEndSequences">EMPPairedEndSequences</option> | |
175 <option value="EMPSingleEndSequences">EMPSingleEndSequences</option> | |
176 <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option> | |
177 <option value="FeatureData[AlignedSequence]">FeatureData[AlignedSequence]</option> | |
178 <option value="FeatureData[Importance]">FeatureData[Importance]</option> | |
179 <option value="FeatureData[PairedEndSequence]">FeatureData[PairedEndSequence]</option> | |
180 <option value="FeatureData[Sequence]">FeatureData[Sequence]</option> | |
181 <option value="FeatureData[Taxonomy]">FeatureData[Taxonomy]</option> | |
182 <option value="FeatureTable[Balance]">FeatureTable[Balance]</option> | |
183 <option value="FeatureTable[Composition]">FeatureTable[Composition]</option> | |
184 <option value="FeatureTable[Frequency]">FeatureTable[Frequency]</option> | |
185 <option value="FeatureTable[PercentileNormalized]">FeatureTable[PercentileNormalized]</option> | |
186 <option value="FeatureTable[PresenceAbsence]">FeatureTable[PresenceAbsence]</option> | |
187 <option value="FeatureTable[RelativeFrequency]">FeatureTable[RelativeFrequency]</option> | |
188 <option value="Hierarchy">Hierarchy</option> | |
189 <option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option> | |
190 <option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option> | |
191 <option value="PCoAResults">PCoAResults</option> | |
192 <option value="Phylogeny[Rooted]">Phylogeny[Rooted]</option> | |
193 <option value="Phylogeny[Unrooted]">Phylogeny[Unrooted]</option> | |
194 <option value="Placements">Placements</option> | |
195 <option value="QualityFilterStats">QualityFilterStats</option> | |
196 <option value="RawSequences">RawSequences</option> | |
197 <option value="SampleData[AlphaDiversity]">SampleData[AlphaDiversity]</option> | |
198 <option value="SampleData[BooleanSeries]">SampleData[BooleanSeries]</option> | |
199 <option value="SampleData[ClassifierPredictions]">SampleData[ClassifierPredictions]</option> | |
200 <option value="SampleData[DADA2Stats]">SampleData[DADA2Stats]</option> | |
201 <option value="SampleData[FirstDifferences]">SampleData[FirstDifferences]</option> | |
202 <option value="SampleData[JoinedSequencesWithQuality]">SampleData[JoinedSequencesWithQuality]</option> | |
203 <option selected="True" value="SampleData[PairedEndSequencesWithQuality]">SampleData[PairedEndSequencesWithQuality]</option> | |
204 <option value="SampleData[RegressorPredictions]">SampleData[RegressorPredictions]</option> | |
205 <option value="SampleData[SequencesWithQuality]">SampleData[SequencesWithQuality]</option> | |
206 <option value="SampleData[Sequences]">SampleData[Sequences]</option> | |
207 <option value="SampleData[Classifier]">SampleData[Classifier]</option> | |
208 <option value="SampleData[Regressor]">SampleData[Regressor]</option> | |
209 <option value="TaxonomicClassifier">TaxonomicClassifier</option> | |
210 <option value="UchimeStats">UchimeStats</option> | |
211 </param> | |
212 | |
213 <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"> | |
214 <option value="AlignedDNAFASTAFormat">AlignedDNAFASTAFormat</option> | |
215 <option value="AlignedDNASequencesDirectoryFormat">AlignedDNASequencesDirectoryFormat</option> | |
216 <option value="AlphaDiversityDirectoryFormat">AlphaDiversityDirectoryFormat</option> | |
217 <option value="AlphaDiversityFormat">AlphaDiversityFormat</option> | |
218 <option value="BIOMV100DirFmt">BIOMV100DirFmt</option> | |
219 <option value="BIOMV100Format">BIOMV100Format</option> | |
220 <option value="BIOMV210DirFmt">BIOMV210DirFmt</option> | |
221 <option value="BIOMV210Format">BIOMV210Format</option> | |
222 <option value="BooleanSeriesDirectoryFormat">BooleanSeriesDirectoryFormat</option> | |
223 <option value="BooleanSeriesFormat">BooleanSeriesFormat</option> | |
224 <option value="CasavaOneEightLanelessPerSampleDirFmt">CasavaOneEightLanelessPerSampleDirFmt</option> | |
225 <option value="CasavaOneEightSingleLanePerSampleDirFmt">CasavaOneEightSingleLanePerSampleDirFmt</option> | |
226 <option value="DADA2StatsDirFmt">DADA2StatsDirFmt</option> | |
227 <option value="DADA2StatsFormat">DADA2StatsFormat</option> | |
228 <option value="DNAFASTAFormat">DNAFASTAFormat</option> | |
229 <option value="DNASequencesDirectoryFormat">DNASequencesDirectoryFormat</option> | |
230 <option value="DeblurStatsDirFmt">DeblurStatsDirFmt</option> | |
231 <option value="DeblurStatsFmt">DeblurStatsFmt</option> | |
232 <option value="DistanceMatrixDirectoryFormat">DistanceMatrixDirectoryFormat</option> | |
233 <option value="EMPPairedEndCasavaDirFmt">EMPPairedEndCasavaDirFmt</option> | |
234 <option value="EMPPairedEndDirFmt">EMPPairedEndDirFmt</option> | |
235 <option value="EMPSingleEndCasavaDirFmt">EMPSingleEndCasavaDirFmt</option> | |
236 <option value="EMPSingleEndDirFmt">EMPSingleEndDirFmt</option> | |
237 <option value="ErrorCorrectionDetailsDirFmt">ErrorCorrectionDetailsDirFmt</option> | |
238 <option value="FastqGzFormat">FastqGzFormat</option> | |
239 <option value="FirstDifferencesDirectoryFormat">FirstDifferencesDirectoryFormat</option> | |
240 <option value="FirstDifferencesFormat">FirstDifferencesFormat</option> | |
241 <option value="HeaderlessTSVTaxonomyDirectoryFormat">HeaderlessTSVTaxonomyDirectoryFormat</option> | |
242 <option value="HeaderlessTSVTaxonomyFormat">HeaderlessTSVTaxonomyFormat</option> | |
243 <option value="ImportanceDirectoryFormat">ImportanceDirectoryFormat</option> | |
244 <option value="ImportanceFormat">ImportanceFormat</option> | |
245 <option value="LSMatFormat">LSMatFormat</option> | |
246 <option value="MultiplexedPairedEndBarcodeInSequenceDirFmt">MultiplexedPairedEndBarcodeInSequenceDirFmt</option> | |
247 <option value="MultiplexedSingleEndBarcodeInSequenceDirFmt">MultiplexedSingleEndBarcodeInSequenceDirFmt</option> | |
248 <option value="NewickDirectoryFormat">NewickDirectoryFormat</option> | |
249 <option value="NewickFormat">NewickFormat</option> | |
250 <option value="OrdinationDirectoryFormat">OrdinationDirectoryFormat</option> | |
251 <option value="OrdinationFormat">OrdinationFormat</option> | |
252 <option value="PairedDNASequencesDirectoryFormat">PairedDNASequencesDirectoryFormat</option> | |
253 <option value="PairedEndFastqManifestPhred33">PairedEndFastqManifestPhred33</option> | |
254 <option value="PairedEndFastqManifestPhred33V2">PairedEndFastqManifestPhred33V2</option> | |
255 <option value="PairedEndFastqManifestPhred64">PairedEndFastqManifestPhred64</option> | |
256 <option value="PairedEndFastqManifestPhred64V2">PairedEndFastqManifestPhred64V2</option> | |
257 <option value="PlacementsDirFmt">PlacementsDirFmt</option> | |
258 <option value="PlacementsFormat">PlacementsFormat</option> | |
259 <option value="PredictionsDirectoryFormat">PredictionsDirectoryFormat</option> | |
260 <option value="PredictionsFormat">PredictionsFormat</option> | |
261 <option value="QIIME1DemuxDirFmt">QIIME1DemuxDirFmt</option> | |
262 <option value="QIIME1DemuxFormat">QIIME1DemuxFormat</option> | |
263 <option value="QualityFilterStatsDirFmt">QualityFilterStatsDirFmt</option> | |
264 <option value="QualityFilterStatsFmt">QualityFilterStatsFmt</option> | |
265 <option value="SampleEstimatorDirFmt">SampleEstimatorDirFmt</option> | |
266 <option value="SingleEndFastqManifestPhred33">SingleEndFastqManifestPhred33</option> | |
267 <option value="SingleEndFastqManifestPhred33V2">SingleEndFastqManifestPhred33V2</option> | |
268 <option value="SingleEndFastqManifestPhred64">SingleEndFastqManifestPhred64</option> | |
269 <option value="SingleEndFastqManifestPhred64V2">SingleEndFastqManifestPhred64V2</option> | |
270 <option value="SingleLanePerSamplePairedEndFastqDirFmt">SingleLanePerSamplePairedEndFastqDirFmt</option> | |
271 <option value="SingleLanePerSampleSingleEndFastqDirFmt">SingleLanePerSampleSingleEndFastqDirFmt</option> | |
272 <option value="TSVTaxonomyDirectoryFormat">TSVTaxonomyDirectoryFormat</option> | |
273 <option value="TSVTaxonomyFormat">TSVTaxonomyFormat</option> | |
274 <option value="TaxonomicClassiferTemporaryPickleDirFmt">TaxonomicClassiferTemporaryPickleDirFmt</option> | |
275 <option value="UchimeStatsDirFmt">UchimeStatsDirFmt</option> | |
276 <option value="UchimeStatsFmt">UchimeStatsFmt</option> | |
277 </param> | |
278 </inputs> | |
279 <outputs> | |
280 <data format="qza" label="${tool.name} on ${on_string}: outputpath.qza" name="outputpath"/> | |
281 </outputs> | |
282 <!--<stdio> | |
283 <exit_code range="2" level="warning" description="Error" /> | |
284 </stdio>--> | |
285 <help> | |
286 </help> | |
287 <macros> | |
288 <import>qiime_citation.xml</import> | |
289 </macros> | |
290 <expand macro="qiime_citation" /> | |
291 </tool> |