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Changeset 0:1370f8d6e95b (2022-08-29)

Next changeset 1:5d9a36073ed6 (2023-01-13)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

added:
qiime2_core__tools__import.xml
test-data/.gitkeep

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

[

b'@@ -0,0 +1,1635 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2022.8.1+dist.h91e3be72.2" profile="22.05" license="BSD-3-Clause">\n+ <description>Import data into a QIIME 2 artifact</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <command>q2galaxy run tools import \'$inputs\'</command>\n+ <configfiles>\n+ <configfile name="inputs"><%\n+# This is an exercise in cheating the Cheetah\n+import json\n+\n+def expand_collection(collection):\n+ # All of this work is just to extract the\n+ # element identifier AND the path\n+ return [dict(name=d.element_identifier, data=stringify(d))\n+ for d in collection]\n+\n+def stringify(obj):\n+ if type(obj) is dict:\n+ new = {}\n+ for key, value in obj.items():\n+ if (key.startswith(\'__\') and key.endswith(\'__\')\n+ and not key.startswith(\'__q2galaxy__\')):\n+ continue\n+ new[str(key)] = stringify(value)\n+\n+ return new\n+ elif type(obj) is list:\n+ return [stringify(x) for x in obj]\n+ elif type(obj.__str__) is not type(object().__str__): # noqa\n+ # There is an associated __str__ which will be used for\n+ # "normal" templating, it looks like a strange check because\n+ # it really is, we\'re testing for method-wrapper as a sign\n+ # of non-implementation\n+ return str(obj)\n+ elif obj.is_collection:\n+ return expand_collection(obj)\n+ else:\n+ raise NotImplementedError("Unrecognized situation in q2galaxy")\n+\n+dataset = self.getVar(\'import_root\')\n+inputs = stringify(dataset)\n+write(json.dumps(inputs))\n+ %></configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="import_root">\n+ <param name="type" type="select" label="Type of data to import:">\n+ <option value="None">Select a QIIME 2 type to import.</option>\n+ <option value="Bowtie2Index">Bowtie2Index</option>\n+ <option value="DeblurStats">DeblurStats</option>\n+ <option value="DistanceMatrix">DistanceMatrix</option>\n+ <option value="EMPPairedEndSequences">EMPPairedEndSequences</option>\n+ <option value="EMPSingleEndSequences">EMPSingleEndSequences</option>\n+ <option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option>\n+ <option value="FeatureData__ob__AlignedProteinSequence__cb__">FeatureData[AlignedProteinSequence]</option>\n+ <option value="FeatureData__ob__AlignedRNASequence__cb__">FeatureData[AlignedRNASequence]</option>\n+ <option value="FeatureData__ob__AlignedSequence__cb__">FeatureData[AlignedSequence]</option>\n+ <option value="FeatureData__ob__BLAST6__cb__">FeatureData[BLAST6]</option>\n+ <option value="FeatureData__ob__Differential__cb__">FeatureData[Differential]</option>\n+ <option value="FeatureData__ob__Importance__cb__">FeatureData[Importance]</option>\n+ <option value="FeatureData__ob__PairedEndRNASequence__cb__">FeatureData[PairedEndRNASequence]</option>\n+ <option value="FeatureData__ob__PairedEndSequence__cb__">FeatureData[PairedEndSequence]</option>\n+ <option value="FeatureData__ob__ProteinSequence__cb__">FeatureData[ProteinSequence]</option>\n+ <option value="FeatureData__ob__RNASequence__cb__">FeatureData[RNASequence]</option>\n+ <option value="FeatureData__ob__Sequence__cb__">FeatureData[Sequence]</option>\n+ <option value="FeatureData__ob__Taxonomy__cb_'..b'nst\n+ the names of the items in that collection. (You may need to append an\n+ extension if your collection\'s element IDs lack one.) Or you can\n+ provide individual history datasets with a filename as in the simpler\n+ cases.\n+\n+Formats:\n+--------\n+These formats have documentation available.\n+\n+HeaderlessTSVTaxonomyFormat\n+***************************\n+Format for a 2+ column TSV file without a header.\n+\n+This format supports comment lines starting with #, and blank lines.\n+\n+\n+TSVTaxonomyFormat\n+*****************\n+Format for a 2+ column TSV file with an expected minimal header.\n+\n+The only header recognized by this format is:\n+\n+ Feature ID<tab>Taxon\n+\n+Optionally followed by other arbitrary columns.\n+\n+This format supports blank lines. The expected header must be the first\n+non-blank line. In addition to the header, there must be at least one line\n+of data.\n+\n+\n+QIIME1DemuxFormat\n+*****************\n+QIIME 1 demultiplexed FASTA format.\n+\n+The QIIME 1 demultiplexed FASTA format is the default output format of\n+``split_libraries.py`` and ``split_libraries_fastq.py``. The file output by\n+QIIME 1 is named ``seqs.fna``; this filename is sometimes associated with\n+the file format itself due to its widespread usage in QIIME 1.\n+\n+The format is documented here:\n+http://qiime.org/documentation/file_formats.html#demultiplexed-sequences\n+\n+Format details:\n+\n+- FASTA file with exactly two lines per record: header and sequence. Each\n+ sequence must span exactly one line and cannot be split across multiple\n+ lines.\n+\n+- The ID in each header must follow the format ``<sample-id>_<seq-id>``.\n+ ``<sample-id>`` is the identifier of the sample the sequence belongs to,\n+ and ``<seq-id>`` is an identifier for the sequence *within* its sample.\n+ In QIIME 1, ``<seq-id>`` is typically an incrementing integer starting\n+ from zero, but any non-empty value can be used here, as long as the\n+ header IDs remain unique throughout the file. Note: ``<sample-id>`` may\n+ contain sample IDs that contain underscores; the rightmost underscore\n+ will used to delimit sample and sequence IDs.\n+\n+- Descriptions in headers are permitted and ignored.\n+\n+- Header IDs must be unique within the file.\n+\n+- Each sequence must be DNA and cannot be empty.\n+\n+\n+FastqGzFormat\n+*************\n+\n+A gzipped fastq file.\n+\n+\n+Additional formats without documentation:\n+*****************************************\n+ - PairedEndFastqManifestPhred64\n+ - SingleEndFastqManifestPhred64\n+ - NewickFormat\n+ - SeppReferenceDirFmt\n+ - PairedRNASequencesDirectoryFormat\n+ - EMPPairedEndDirFmt\n+ - ArtificialGroupingFormat\n+ - BLAST6Format\n+ - CasavaOneEightLanelessPerSampleDirFmt\n+ - ProbabilitiesFormat\n+ - PlacementsFormat\n+ - DADA2StatsFormat\n+ - SampleEstimatorDirFmt\n+ - ImportanceFormat\n+ - AlignedProteinFASTAFormat\n+ - SingleLanePerSampleSingleEndFastqDirFmt\n+ - BIOMV210Format\n+ - PairedEndFastqManifestPhred33V2\n+ - CasavaOneEightSingleLanePerSampleDirFmt\n+ - ProteinFASTAFormat\n+ - SingleEndFastqManifestPhred64V2\n+ - Bowtie2IndexDirFmt\n+ - DifferentialFormat\n+ - UchimeStatsFmt\n+ - DeblurStatsFmt\n+ - PairedEndFastqManifestPhred33\n+ - AlignedRNAFASTAFormat\n+ - EMPSingleEndDirFmt\n+ - SingleEndFastqManifestPhred33\n+ - AlignedDNAFASTAFormat\n+ - EMPPairedEndCasavaDirFmt\n+ - ProcrustesStatisticsFmt\n+ - FirstDifferencesFormat\n+ - BIOMV100Format\n+ - PairedDNASequencesDirectoryFormat\n+ - MultiplexedPairedEndBarcodeInSequenceDirFmt\n+ - AlphaDiversityFormat\n+ - LSMatFormat\n+ - BooleanSeriesFormat\n+ - OrdinationFormat\n+ - SingleLanePerSamplePairedEndFastqDirFmt\n+ - PairedEndFastqManifestPhred64V2\n+ - RNAFASTAFormat\n+ - TaxonomicClassiferTemporaryPickleDirFmt\n+ - PredictionsFormat\n+ - DNAFASTAFormat\n+ - QualityFilterStatsFmt\n+ - ErrorCorrectionDetailsFmt\n+ - EMPSingleEndCasavaDirFmt\n+ - SingleEndFastqManifestPhred33V2\n+</help>\n+ <citations>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'