# HG changeset patch # User q2d2 # Date 1661805418 0 # Node ID 1370f8d6e95bdd3e360fb5db53f74de52136ffc9 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 diff -r 000000000000 -r 1370f8d6e95b qiime2_core__tools__import.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2_core__tools__import.xml Mon Aug 29 20:36:58 2022 +0000 @@ -0,0 +1,1635 @@ + + + + + Import data into a QIIME 2 artifact + + quay.io/qiime2/core:2022.8 + + q2galaxy run tools import '$inputs' + + <% +# This is an exercise in cheating the Cheetah +import json + +def expand_collection(collection): + # All of this work is just to extract the + # element identifier AND the path + return [dict(name=d.element_identifier, data=stringify(d)) + for d in collection] + +def stringify(obj): + if type(obj) is dict: + new = {} + for key, value in obj.items(): + if (key.startswith('__') and key.endswith('__') + and not key.startswith('__q2galaxy__')): + continue + new[str(key)] = stringify(value) + + return new + elif type(obj) is list: + return [stringify(x) for x in obj] + elif type(obj.__str__) is not type(object().__str__): # noqa + # There is an associated __str__ which will be used for + # "normal" templating, it looks like a strange check because + # it really is, we're testing for method-wrapper as a sign + # of non-implementation + return str(obj) + elif obj.is_collection: + return expand_collection(obj) + else: + raise NotImplementedError("Unrecognized situation in q2galaxy") + +dataset = self.getVar('import_root') +inputs = stringify(dataset) +write(json.dumps(inputs)) + %> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + + + + + + +QIIME 2: tools import +===================== +Import data as a QIIME 2 artifact + +Instructions +------------ + + 1. Select the type you wish to import. If you are uncertain, consider what + your next action would be and identify what type it requires. + + 2. Identify which format will best suite the data you have available. Many + types will have only a single format available. There is some documentation + available below on the different formats, however there may not be + very much documentation available for your format. + + 3. For each part of the format, you will need to associate some data. + + a. If it is a simple format, you may just select the history dataset. + b. If it is a more complex format, you will need to provide either a + filename and history dataset, or a collection. + c. For collections, they can be constructed via matching a regex against + the names of the items in that collection. (You may need to append an + extension if your collection's element IDs lack one.) Or you can + provide individual history datasets with a filename as in the simpler + cases. + +Formats: +-------- +These formats have documentation available. + +HeaderlessTSVTaxonomyFormat +*************************** +Format for a 2+ column TSV file without a header. + +This format supports comment lines starting with #, and blank lines. + + +TSVTaxonomyFormat +***************** +Format for a 2+ column TSV file with an expected minimal header. + +The only header recognized by this format is: + + Feature ID<tab>Taxon + +Optionally followed by other arbitrary columns. + +This format supports blank lines. The expected header must be the first +non-blank line. In addition to the header, there must be at least one line +of data. + + +QIIME1DemuxFormat +***************** +QIIME 1 demultiplexed FASTA format. + +The QIIME 1 demultiplexed FASTA format is the default output format of +``split_libraries.py`` and ``split_libraries_fastq.py``. The file output by +QIIME 1 is named ``seqs.fna``; this filename is sometimes associated with +the file format itself due to its widespread usage in QIIME 1. + +The format is documented here: +http://qiime.org/documentation/file_formats.html#demultiplexed-sequences + +Format details: + +- FASTA file with exactly two lines per record: header and sequence. Each + sequence must span exactly one line and cannot be split across multiple + lines. + +- The ID in each header must follow the format ``<sample-id>_<seq-id>``. + ``<sample-id>`` is the identifier of the sample the sequence belongs to, + and ``<seq-id>`` is an identifier for the sequence *within* its sample. + In QIIME 1, ``<seq-id>`` is typically an incrementing integer starting + from zero, but any non-empty value can be used here, as long as the + header IDs remain unique throughout the file. Note: ``<sample-id>`` may + contain sample IDs that contain underscores; the rightmost underscore + will used to delimit sample and sequence IDs. + +- Descriptions in headers are permitted and ignored. + +- Header IDs must be unique within the file. + +- Each sequence must be DNA and cannot be empty. + + +FastqGzFormat +************* + +A gzipped fastq file. + + +Additional formats without documentation: +***************************************** + - PairedEndFastqManifestPhred64 + - SingleEndFastqManifestPhred64 + - NewickFormat + - SeppReferenceDirFmt + - PairedRNASequencesDirectoryFormat + - EMPPairedEndDirFmt + - ArtificialGroupingFormat + - BLAST6Format + - CasavaOneEightLanelessPerSampleDirFmt + - ProbabilitiesFormat + - PlacementsFormat + - DADA2StatsFormat + - SampleEstimatorDirFmt + - ImportanceFormat + - AlignedProteinFASTAFormat + - SingleLanePerSampleSingleEndFastqDirFmt + - BIOMV210Format + - PairedEndFastqManifestPhred33V2 + - CasavaOneEightSingleLanePerSampleDirFmt + - ProteinFASTAFormat + - SingleEndFastqManifestPhred64V2 + - Bowtie2IndexDirFmt + - DifferentialFormat + - UchimeStatsFmt + - DeblurStatsFmt + - PairedEndFastqManifestPhred33 + - AlignedRNAFASTAFormat + - EMPSingleEndDirFmt + - SingleEndFastqManifestPhred33 + - AlignedDNAFASTAFormat + - EMPPairedEndCasavaDirFmt + - ProcrustesStatisticsFmt + - FirstDifferencesFormat + - BIOMV100Format + - PairedDNASequencesDirectoryFormat + - MultiplexedPairedEndBarcodeInSequenceDirFmt + - AlphaDiversityFormat + - LSMatFormat + - BooleanSeriesFormat + - OrdinationFormat + - SingleLanePerSamplePairedEndFastqDirFmt + - PairedEndFastqManifestPhred64V2 + - RNAFASTAFormat + - TaxonomicClassiferTemporaryPickleDirFmt + - PredictionsFormat + - DNAFASTAFormat + - QualityFilterStatsFmt + - ErrorCorrectionDetailsFmt + - EMPSingleEndCasavaDirFmt + - SingleEndFastqManifestPhred33V2 + + + 10.1038/s41587-019-0209-9 + + diff -r 000000000000 -r 1370f8d6e95b test-data/.gitkeep