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comparison qiime2_core__tools__import.xml @ 1:5d9a36073ed6 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 23:02:20 +0000
parents 1370f8d6e95b
children 18c6b2b6740f
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0:1370f8d6e95b 1:5d9a36073ed6
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2022, QIIME 2 development team. 3 Copyright (c) 2023, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1) 9 q2galaxy (version: 2022.11.1)
10 for: 10 for:
11 qiime2 (version: 2022.8.1) 11 qiime2 (version: 2022.11.1)
12 --> 12 -->
13 <tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.11.1+dist.h2bda5906.2" profile="22.05" license="BSD-3-Clause">
14 <description>Import data into a QIIME 2 artifact</description> 14 <description>Import data into a QIIME 2 artifact</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container> 16 <container type="docker">quay.io/qiime2/core:2022.11</container>
17 </requirements> 17 </requirements>
18 <command>q2galaxy run tools import '$inputs'</command> 18 <command detect_errors="exit_code">q2galaxy run tools import '$inputs'</command>
19 <configfiles> 19 <configfiles>
20 <configfile name="inputs">&lt;% 20 <configfile name="inputs">&lt;%
21 # This is an exercise in cheating the Cheetah 21 # This is an exercise in cheating the Cheetah
22 import json 22 import json
23 23
67 <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option> 67 <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option>
68 <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option> 68 <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option>
69 <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option> 69 <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option>
70 <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option> 70 <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option>
71 <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option> 71 <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option>
72 <option value="FeatureData__ob__DifferentialAbundance__cb__">FeatureData[DifferentialAbundance]</option>
72 <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option> 73 <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option>
73 <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option> 74 <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option>
74 <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option> 75 <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option>
75 <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option> 76 <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option>
76 <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option> 77 <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option>
277 </when> 278 </when>
278 <when value="FeatureData__ob__AlignedRNASequence__cb__"> 279 <when value="FeatureData__ob__AlignedRNASequence__cb__">
279 <conditional name="__q2galaxy__GUI__cond__format__"> 280 <conditional name="__q2galaxy__GUI__cond__format__">
280 <param name="format" type="select" label="QIIME 2 file format to import from:"> 281 <param name="format" type="select" label="QIIME 2 file format to import from:">
281 <option value="AlignedRNAFASTAFormat" selected="true">Aligned RNAFASTA Format</option> 282 <option value="AlignedRNAFASTAFormat" selected="true">Aligned RNAFASTA Format</option>
283 <option value="MixedCaseAlignedRNAFASTAFormat" selected="false">Mixed Case Aligned RNAFASTA Format</option>
282 </param> 284 </param>
283 <when value="AlignedRNAFASTAFormat"> 285 <when value="AlignedRNAFASTAFormat">
284 <section name="import" expanded="true" title="Import"> 286 <section name="import" expanded="true" title="Import">
285 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 287 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
286 <param name="data" type="data" format="data" help="This data should be formatted as a AlignedRNAFASTAFormat. See the documentation below for more information."/> 288 <param name="data" type="data" format="data" help="This data should be formatted as a AlignedRNAFASTAFormat. See the documentation below for more information."/>
287 </section> 289 </section>
288 </when> 290 </when>
291 <when value="MixedCaseAlignedRNAFASTAFormat">
292 <section name="import" expanded="true" title="Import">
293 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
294 <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseAlignedRNAFASTAFormat. See the documentation below for more information."/>
295 </section>
296 </when>
289 </conditional> 297 </conditional>
290 </when> 298 </when>
291 <when value="FeatureData__ob__AlignedSequence__cb__"> 299 <when value="FeatureData__ob__AlignedSequence__cb__">
292 <conditional name="__q2galaxy__GUI__cond__format__"> 300 <conditional name="__q2galaxy__GUI__cond__format__">
293 <param name="format" type="select" label="QIIME 2 file format to import from:"> 301 <param name="format" type="select" label="QIIME 2 file format to import from:">
294 <option value="AlignedDNAFASTAFormat" selected="true">Aligned DNAFASTA Format</option> 302 <option value="AlignedDNAFASTAFormat" selected="true">Aligned DNAFASTA Format</option>
303 <option value="MixedCaseAlignedDNAFASTAFormat" selected="false">Mixed Case Aligned DNAFASTA Format</option>
295 </param> 304 </param>
296 <when value="AlignedDNAFASTAFormat"> 305 <when value="AlignedDNAFASTAFormat">
297 <section name="import" expanded="true" title="Import"> 306 <section name="import" expanded="true" title="Import">
298 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 307 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
299 <param name="data" type="data" format="data" help="This data should be formatted as a AlignedDNAFASTAFormat. See the documentation below for more information."/> 308 <param name="data" type="data" format="data" help="This data should be formatted as a AlignedDNAFASTAFormat. See the documentation below for more information."/>
300 </section> 309 </section>
301 </when> 310 </when>
311 <when value="MixedCaseAlignedDNAFASTAFormat">
312 <section name="import" expanded="true" title="Import">
313 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
314 <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseAlignedDNAFASTAFormat. See the documentation below for more information."/>
315 </section>
316 </when>
302 </conditional> 317 </conditional>
303 </when> 318 </when>
304 <when value="FeatureData__ob__BLAST6__cb__"> 319 <when value="FeatureData__ob__BLAST6__cb__">
305 <conditional name="__q2galaxy__GUI__cond__format__"> 320 <conditional name="__q2galaxy__GUI__cond__format__">
306 <param name="format" type="select" label="QIIME 2 file format to import from:"> 321 <param name="format" type="select" label="QIIME 2 file format to import from:">
308 </param> 323 </param>
309 <when value="BLAST6Format"> 324 <when value="BLAST6Format">
310 <section name="import" expanded="true" title="Import"> 325 <section name="import" expanded="true" title="Import">
311 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 326 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
312 <param name="data" type="data" format="data" help="This data should be formatted as a BLAST6Format. See the documentation below for more information."/> 327 <param name="data" type="data" format="data" help="This data should be formatted as a BLAST6Format. See the documentation below for more information."/>
328 </section>
329 </when>
330 </conditional>
331 </when>
332 <when value="FeatureData__ob__DifferentialAbundance__cb__">
333 <conditional name="__q2galaxy__GUI__cond__format__">
334 <param name="format" type="select" label="QIIME 2 file format to import from:">
335 <option value="DataLoafPackageDirFmt" selected="true">Data Loaf Package Directory Format</option>
336 </param>
337 <when value="DataLoafPackageDirFmt">
338 <section name="import_data_slices" expanded="true" title="Import data_slices">
339 <conditional name="__q2galaxy__GUI__cond__data_slices__">
340 <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
341 <option value="collection" selected="true">Use collection to import</option>
342 <option value="individual">Associate individual files</option>
343 </param>
344 <when value="collection">
345 <param name="elements" type="data_collection" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\.csv"/>
346 <conditional name="__q2galaxy__GUI__cond__add_ext__">
347 <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
348 <option value="no">No, use element identifiers as is</option>
349 <option value="yes">Yes, append an extension</option>
350 </param>
351 <when value="yes">
352 <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
353 </when>
354 <when value="no"/>
355 </conditional>
356 </when>
357 <when value="individual">
358 <repeat name="elements" min="1" title="Add Elements">
359 <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.csv">
360 <validator type="regex" message="This filename doesn't match the regex.">.+\.csv</validator>
361 </param>
362 <param name="data" type="data" format="data" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information."/>
363 </repeat>
364 </when>
365 </conditional>
366 </section>
367 <section name="import_nutrition_facts" expanded="true" title="Import nutrition_facts">
368 <param name="name" type="text" value="datapackage.json" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
369 <param name="data" type="data" format="data" help="This data should be formatted as a DataPackageSchemaFileFormat. See the documentation below for more information."/>
313 </section> 370 </section>
314 </when> 371 </when>
315 </conditional> 372 </conditional>
316 </when> 373 </when>
317 <when value="FeatureData__ob__Differential__cb__"> 374 <when value="FeatureData__ob__Differential__cb__">
388 </conditional> 445 </conditional>
389 </when> 446 </when>
390 <when value="FeatureData__ob__RNASequence__cb__"> 447 <when value="FeatureData__ob__RNASequence__cb__">
391 <conditional name="__q2galaxy__GUI__cond__format__"> 448 <conditional name="__q2galaxy__GUI__cond__format__">
392 <param name="format" type="select" label="QIIME 2 file format to import from:"> 449 <param name="format" type="select" label="QIIME 2 file format to import from:">
450 <option value="MixedCaseRNAFASTAFormat" selected="false">Mixed Case RNAFASTA Format</option>
393 <option value="RNAFASTAFormat" selected="true">RNAFASTA Format</option> 451 <option value="RNAFASTAFormat" selected="true">RNAFASTA Format</option>
394 </param> 452 </param>
453 <when value="MixedCaseRNAFASTAFormat">
454 <section name="import" expanded="true" title="Import">
455 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
456 <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseRNAFASTAFormat. See the documentation below for more information."/>
457 </section>
458 </when>
395 <when value="RNAFASTAFormat"> 459 <when value="RNAFASTAFormat">
396 <section name="import" expanded="true" title="Import"> 460 <section name="import" expanded="true" title="Import">
397 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 461 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
398 <param name="data" type="data" format="data" help="This data should be formatted as a RNAFASTAFormat. See the documentation below for more information."/> 462 <param name="data" type="data" format="data" help="This data should be formatted as a RNAFASTAFormat. See the documentation below for more information."/>
399 </section> 463 </section>
402 </when> 466 </when>
403 <when value="FeatureData__ob__Sequence__cb__"> 467 <when value="FeatureData__ob__Sequence__cb__">
404 <conditional name="__q2galaxy__GUI__cond__format__"> 468 <conditional name="__q2galaxy__GUI__cond__format__">
405 <param name="format" type="select" label="QIIME 2 file format to import from:"> 469 <param name="format" type="select" label="QIIME 2 file format to import from:">
406 <option value="DNAFASTAFormat" selected="true">DNAFASTA Format</option> 470 <option value="DNAFASTAFormat" selected="true">DNAFASTA Format</option>
471 <option value="MixedCaseDNAFASTAFormat" selected="false">Mixed Case DNAFASTA Format</option>
407 </param> 472 </param>
408 <when value="DNAFASTAFormat"> 473 <when value="DNAFASTAFormat">
409 <section name="import" expanded="true" title="Import"> 474 <section name="import" expanded="true" title="Import">
410 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 475 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
411 <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/> 476 <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
477 </section>
478 </when>
479 <when value="MixedCaseDNAFASTAFormat">
480 <section name="import" expanded="true" title="Import">
481 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
482 <param name="data" type="data" format="data" help="This data should be formatted as a MixedCaseDNAFASTAFormat. See the documentation below for more information."/>
412 </section> 483 </section>
413 </when> 484 </when>
414 </conditional> 485 </conditional>
415 </when> 486 </when>
416 <when value="FeatureData__ob__Taxonomy__cb__"> 487 <when value="FeatureData__ob__Taxonomy__cb__">
612 </when> 683 </when>
613 <when value="MultiplexedSingleEndBarcodeInSequence"> 684 <when value="MultiplexedSingleEndBarcodeInSequence">
614 <conditional name="__q2galaxy__GUI__cond__format__"> 685 <conditional name="__q2galaxy__GUI__cond__format__">
615 <param name="format" type="select" label="QIIME 2 file format to import from:"> 686 <param name="format" type="select" label="QIIME 2 file format to import from:">
616 <option value="FastqGzFormat" selected="true">Fastq Gz Format</option> 687 <option value="FastqGzFormat" selected="true">Fastq Gz Format</option>
688 <option value="MultiplexedFastaQualDirFmt" selected="false">Multiplexed Fasta Qual Directory Format</option>
617 </param> 689 </param>
618 <when value="FastqGzFormat"> 690 <when value="FastqGzFormat">
619 <section name="import" expanded="true" title="Import"> 691 <section name="import" expanded="true" title="Import">
620 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 692 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
621 <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/> 693 <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/>
694 </section>
695 </when>
696 <when value="MultiplexedFastaQualDirFmt">
697 <section name="import_sequences" expanded="true" title="Import sequences">
698 <param name="name" type="text" value="reads.fasta" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
699 <param name="data" type="data" format="data" help="This data should be formatted as a DNAFASTAFormat. See the documentation below for more information."/>
700 </section>
701 <section name="import_quality" expanded="true" title="Import quality">
702 <param name="name" type="text" value="reads.qual" help="Filename to import the data as. You shouldn't need to change this unless something is wrong."/>
703 <param name="data" type="data" format="data" help="This data should be formatted as a QualFormat. See the documentation below for more information."/>
622 </section> 704 </section>
623 </when> 705 </when>
624 </conditional> 706 </conditional>
625 </when> 707 </when>
626 <when value="PCoAResults"> 708 <when value="PCoAResults">
810 <when value="SampleData__ob__JoinedSequencesWithQuality__cb__"> 892 <when value="SampleData__ob__JoinedSequencesWithQuality__cb__">
811 <conditional name="__q2galaxy__GUI__cond__format__"> 893 <conditional name="__q2galaxy__GUI__cond__format__">
812 <param name="format" type="select" label="QIIME 2 file format to import from:"> 894 <param name="format" type="select" label="QIIME 2 file format to import from:">
813 <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option> 895 <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option>
814 <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option> 896 <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option>
897 <option value="SampleIdIndexedSingleEndPerSampleDirFmt" selected="false">Sample Id Indexed Single End Per Sample Directory Format</option>
815 <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option> 898 <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option>
816 <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option> 899 <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option>
817 <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option> 900 <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option>
818 <option value="SingleEndFastqManifestPhred64V2" selected="false">Single End Fastq Manifest Phred64V2</option> 901 <option value="SingleEndFastqManifestPhred64V2" selected="false">Single End Fastq Manifest Phred64V2</option>
819 <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="false">Single Lane Per Sample Paired End Fastq Directory Format</option> 902 <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="false">Single Lane Per Sample Paired End Fastq Directory Format</option>
879 </repeat> 962 </repeat>
880 </when> 963 </when>
881 </conditional> 964 </conditional>
882 </section> 965 </section>
883 </when> 966 </when>
967 <when value="SampleIdIndexedSingleEndPerSampleDirFmt">
968 <section name="import_sequences" expanded="true" title="Import sequences">
969 <conditional name="__q2galaxy__GUI__cond__sequences__">
970 <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
971 <option value="collection" selected="true">Use collection to import</option>
972 <option value="individual">Associate individual files</option>
973 </param>
974 <when value="collection">
975 <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/>
976 <conditional name="__q2galaxy__GUI__cond__add_ext__">
977 <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
978 <option value="no">No, use element identifiers as is</option>
979 <option value="yes">Yes, append an extension</option>
980 </param>
981 <when value="yes">
982 <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
983 </when>
984 <when value="no"/>
985 </conditional>
986 </when>
987 <when value="individual">
988 <repeat name="elements" min="1" title="Add Elements">
989 <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.fastq\.gz">
990 <validator type="regex" message="This filename doesn't match the regex.">.+\.fastq\.gz</validator>
991 </param>
992 <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/>
993 </repeat>
994 </when>
995 </conditional>
996 </section>
997 </when>
884 <when value="SingleEndFastqManifestPhred33"> 998 <when value="SingleEndFastqManifestPhred33">
885 <section name="import" expanded="true" title="Import"> 999 <section name="import" expanded="true" title="Import">
886 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 1000 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
887 <param name="data" type="data" format="data" help="This data should be formatted as a SingleEndFastqManifestPhred33. See the documentation below for more information."/> 1001 <param name="data" type="data" format="data" help="This data should be formatted as a SingleEndFastqManifestPhred33. See the documentation below for more information."/>
888 </section> 1002 </section>
1152 <when value="SampleData__ob__SequencesWithQuality__cb__"> 1266 <when value="SampleData__ob__SequencesWithQuality__cb__">
1153 <conditional name="__q2galaxy__GUI__cond__format__"> 1267 <conditional name="__q2galaxy__GUI__cond__format__">
1154 <param name="format" type="select" label="QIIME 2 file format to import from:"> 1268 <param name="format" type="select" label="QIIME 2 file format to import from:">
1155 <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option> 1269 <option value="CasavaOneEightLanelessPerSampleDirFmt" selected="false">Casava One Eight Laneless Per Sample Directory Format</option>
1156 <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option> 1270 <option value="CasavaOneEightSingleLanePerSampleDirFmt" selected="false">Casava One Eight Single Lane Per Sample Directory Format</option>
1271 <option value="SampleIdIndexedSingleEndPerSampleDirFmt" selected="false">Sample Id Indexed Single End Per Sample Directory Format</option>
1157 <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option> 1272 <option value="SingleEndFastqManifestPhred33" selected="false">Single End Fastq Manifest Phred33</option>
1158 <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option> 1273 <option value="SingleEndFastqManifestPhred33V2" selected="false">Single End Fastq Manifest Phred33V2</option>
1159 <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option> 1274 <option value="SingleEndFastqManifestPhred64" selected="false">Single End Fastq Manifest Phred64</option>
1160 <option value="SingleEndFastqManifestPhred64V2" selected="false">Single End Fastq Manifest Phred64V2</option> 1275 <option value="SingleEndFastqManifestPhred64V2" selected="false">Single End Fastq Manifest Phred64V2</option>
1161 <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="false">Single Lane Per Sample Paired End Fastq Directory Format</option> 1276 <option value="SingleLanePerSamplePairedEndFastqDirFmt" selected="false">Single Lane Per Sample Paired End Fastq Directory Format</option>
1221 </repeat> 1336 </repeat>
1222 </when> 1337 </when>
1223 </conditional> 1338 </conditional>
1224 </section> 1339 </section>
1225 </when> 1340 </when>
1341 <when value="SampleIdIndexedSingleEndPerSampleDirFmt">
1342 <section name="import_sequences" expanded="true" title="Import sequences">
1343 <conditional name="__q2galaxy__GUI__cond__sequences__">
1344 <param name="__q2galaxy__GUI__select__picker__" type="select" label="Select a mechanism">
1345 <option value="collection" selected="true">Use collection to import</option>
1346 <option value="individual">Associate individual files</option>
1347 </param>
1348 <when value="collection">
1349 <param name="elements" type="data_collection" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+\.fastq\.gz"/>
1350 <conditional name="__q2galaxy__GUI__cond__add_ext__">
1351 <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">
1352 <option value="no">No, use element identifiers as is</option>
1353 <option value="yes">Yes, append an extension</option>
1354 </param>
1355 <when value="yes">
1356 <param name="ext" type="text" label="Extension to append (e.g. '.fastq.gz')"/>
1357 </when>
1358 <when value="no"/>
1359 </conditional>
1360 </when>
1361 <when value="individual">
1362 <repeat name="elements" min="1" title="Add Elements">
1363 <param name="name" type="text" help="Filename to import the data as. Must match regex: .+\.fastq\.gz">
1364 <validator type="regex" message="This filename doesn't match the regex.">.+\.fastq\.gz</validator>
1365 </param>
1366 <param name="data" type="data" format="data" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information."/>
1367 </repeat>
1368 </when>
1369 </conditional>
1370 </section>
1371 </when>
1226 <when value="SingleEndFastqManifestPhred33"> 1372 <when value="SingleEndFastqManifestPhred33">
1227 <section name="import" expanded="true" title="Import"> 1373 <section name="import" expanded="true" title="Import">
1228 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/> 1374 <param name="name" type="hidden" value="__q2galaxy__::literal::None"/>
1229 <param name="data" type="data" format="data" help="This data should be formatted as a SingleEndFastqManifestPhred33. See the documentation below for more information."/> 1375 <param name="data" type="data" format="data" help="This data should be formatted as a SingleEndFastqManifestPhred33. See the documentation below for more information."/>
1230 </section> 1376 </section>
1512 1658
1513 Formats: 1659 Formats:
1514 -------- 1660 --------
1515 These formats have documentation available. 1661 These formats have documentation available.
1516 1662
1517 HeaderlessTSVTaxonomyFormat 1663 SampleIdIndexedSingleEndPerSampleDirFmt
1518 *************************** 1664 ***************************************
1519 Format for a 2+ column TSV file without a header. 1665 Single-end reads in fastq.gz files where base filename is the sample id
1520 1666
1521 This format supports comment lines starting with #, and blank lines. 1667 The full file name, minus the extension (`.fastq.gz`) is the sample id.
1522 1668 For example, the sample id for the file:
1669 * `sample-1.fastq.gz` is `sample-1`
1670 * `xyz.fastq.gz` is `xyz`
1671 * `sample-42_S1_L001_R1_001.fastq.gz` is `sample-42_S1_L001_R1_001`
1523 1672
1524 TSVTaxonomyFormat 1673 TSVTaxonomyFormat
1525 ***************** 1674 *****************
1526 Format for a 2+ column TSV file with an expected minimal header. 1675 Format for a 2+ column TSV file with an expected minimal header.
1527 1676
1568 - Header IDs must be unique within the file. 1717 - Header IDs must be unique within the file.
1569 1718
1570 - Each sequence must be DNA and cannot be empty. 1719 - Each sequence must be DNA and cannot be empty.
1571 1720
1572 1721
1722 HeaderlessTSVTaxonomyFormat
1723 ***************************
1724 Format for a 2+ column TSV file without a header.
1725
1726 This format supports comment lines starting with #, and blank lines.
1727
1728
1573 FastqGzFormat 1729 FastqGzFormat
1574 ************* 1730 *************
1575 1731
1576 A gzipped fastq file. 1732 A gzipped fastq file.
1577 1733
1578 1734
1579 Additional formats without documentation: 1735 Additional formats without documentation:
1580 ***************************************** 1736 *****************************************
1737 - MixedCaseAlignedDNAFASTAFormat
1738 - DeblurStatsFmt
1739 - DADA2StatsFormat
1581 - PairedEndFastqManifestPhred64 1740 - PairedEndFastqManifestPhred64
1741 - BIOMV210Format
1742 - AlignedDNAFASTAFormat
1743 - DataLoafPackageDirFmt
1582 - SingleEndFastqManifestPhred64 1744 - SingleEndFastqManifestPhred64
1745 - PairedDNASequencesDirectoryFormat
1746 - BLAST6Format
1747 - EMPPairedEndDirFmt
1748 - PlacementsFormat
1749 - AlignedProteinFASTAFormat
1750 - MixedCaseRNAFASTAFormat
1751 - FirstDifferencesFormat
1752 - CasavaOneEightLanelessPerSampleDirFmt
1753 - Bowtie2IndexDirFmt
1754 - EMPSingleEndCasavaDirFmt
1755 - ProcrustesStatisticsFmt
1756 - ProteinFASTAFormat
1757 - RNAFASTAFormat
1758 - SingleLanePerSampleSingleEndFastqDirFmt
1759 - PairedEndFastqManifestPhred33V2
1760 - OrdinationFormat
1761 - MixedCaseDNAFASTAFormat
1762 - TaxonomicClassiferTemporaryPickleDirFmt
1763 - ArtificialGroupingFormat
1764 - BIOMV100Format
1765 - CasavaOneEightSingleLanePerSampleDirFmt
1766 - ErrorCorrectionDetailsFmt
1767 - ImportanceFormat
1768 - SingleEndFastqManifestPhred33V2
1769 - DNAFASTAFormat
1770 - MultiplexedFastaQualDirFmt
1771 - PredictionsFormat
1772 - MultiplexedPairedEndBarcodeInSequenceDirFmt
1773 - PairedEndFastqManifestPhred33
1774 - AlphaDiversityFormat
1775 - ProbabilitiesFormat
1776 - EMPSingleEndDirFmt
1777 - PairedRNASequencesDirectoryFormat
1778 - SingleEndFastqManifestPhred33
1779 - UchimeStatsFmt
1780 - EMPPairedEndCasavaDirFmt
1583 - NewickFormat 1781 - NewickFormat
1782 - SampleEstimatorDirFmt
1783 - DifferentialFormat
1784 - LSMatFormat
1785 - SingleLanePerSamplePairedEndFastqDirFmt
1786 - QualityFilterStatsFmt
1787 - PairedEndFastqManifestPhred64V2
1788 - MixedCaseAlignedRNAFASTAFormat
1789 - SingleEndFastqManifestPhred64V2
1790 - AlignedRNAFASTAFormat
1791 - BooleanSeriesFormat
1584 - SeppReferenceDirFmt 1792 - SeppReferenceDirFmt
1585 - PairedRNASequencesDirectoryFormat
1586 - EMPPairedEndDirFmt
1587 - ArtificialGroupingFormat
1588 - BLAST6Format
1589 - CasavaOneEightLanelessPerSampleDirFmt
1590 - ProbabilitiesFormat
1591 - PlacementsFormat
1592 - DADA2StatsFormat
1593 - SampleEstimatorDirFmt
1594 - ImportanceFormat
1595 - AlignedProteinFASTAFormat
1596 - SingleLanePerSampleSingleEndFastqDirFmt
1597 - BIOMV210Format
1598 - PairedEndFastqManifestPhred33V2
1599 - CasavaOneEightSingleLanePerSampleDirFmt
1600 - ProteinFASTAFormat
1601 - SingleEndFastqManifestPhred64V2
1602 - Bowtie2IndexDirFmt
1603 - DifferentialFormat
1604 - UchimeStatsFmt
1605 - DeblurStatsFmt
1606 - PairedEndFastqManifestPhred33
1607 - AlignedRNAFASTAFormat
1608 - EMPSingleEndDirFmt
1609 - SingleEndFastqManifestPhred33
1610 - AlignedDNAFASTAFormat
1611 - EMPPairedEndCasavaDirFmt
1612 - ProcrustesStatisticsFmt
1613 - FirstDifferencesFormat
1614 - BIOMV100Format
1615 - PairedDNASequencesDirectoryFormat
1616 - MultiplexedPairedEndBarcodeInSequenceDirFmt
1617 - AlphaDiversityFormat
1618 - LSMatFormat
1619 - BooleanSeriesFormat
1620 - OrdinationFormat
1621 - SingleLanePerSamplePairedEndFastqDirFmt
1622 - PairedEndFastqManifestPhred64V2
1623 - RNAFASTAFormat
1624 - TaxonomicClassiferTemporaryPickleDirFmt
1625 - PredictionsFormat
1626 - DNAFASTAFormat
1627 - QualityFilterStatsFmt
1628 - ErrorCorrectionDetailsFmt
1629 - EMPSingleEndCasavaDirFmt
1630 - SingleEndFastqManifestPhred33V2
1631 </help> 1793 </help>
1632 <citations> 1794 <citations>
1633 <citation type="doi">10.1038/s41587-019-0209-9</citation> 1795 <citation type="doi">10.1038/s41587-019-0209-9</citation>
1634 </citations> 1796 </citations>
1635 </tool> 1797 </tool>