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comparison qiime2/qiime_tools_import.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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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>