| Previous changeset 2:18c6b2b6740f (2023-06-08) Next changeset 4:9dbdf05beaa9 (2024-04-25) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit db44258c63cb7e98d605a94464066fc8a5ef75ac |
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modified:
qiime2_core__tools__import.xml |
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added:
test-data/YY/YY_S49_R1_001.fastq.gz test-data/YY/YY_S49_R2_001.fastq.gz |
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| diff -r 18c6b2b6740f -r 10447a4b0cc3 qiime2_core__tools__import.xml --- a/qiime2_core__tools__import.xml Thu Jun 08 19:53:28 2023 +0000 +++ b/qiime2_core__tools__import.xml Thu Feb 01 21:22:08 2024 +0000 |
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| b'@@ -10,7 +10,7 @@\n for:\n qiime2 (version: 2023.5.1)\n -->\n-<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause">\n+<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" 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:2023.5</container>\n@@ -20,6 +20,7 @@\n <configfile name="inputs"><%\n # This is an exercise in cheating the Cheetah\n import json\n+from collections.abc import MutableMapping\n \n def expand_collection(collection):\n # All of this work is just to extract the\n@@ -28,7 +29,7 @@\n for d in collection]\n \n def stringify(obj):\n- if type(obj) is dict:\n+ if isinstance(obj, MutableMapping):\n new = {}\n for key, value in obj.items():\n if (key.startswith(\'__\') and key.endswith(\'__\')\n@@ -357,7 +358,7 @@\n <option value="individual">Associate individual files</option>\n </param>\n <when value="collection">\n- <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"/>\n+ <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FrictionlessCSVFileFormat. See the documentation below for more information. Elements must match regex: .+\\.csv"/>\n <conditional name="__q2galaxy__GUI__cond__add_ext__">\n <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">\n <option value="no">No, use element identifiers as is</option>\n@@ -938,7 +939,7 @@\n <option value="individual">Associate individual files</option>\n </param>\n <when value="collection">\n- <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: .+_.+_R[12]_001\\.fastq\\.gz"/>\n+ <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_R[12]_001\\.fastq\\.gz"/>\n <conditional name="__q2galaxy__GUI__cond__add_ext__">\n <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">\n <option value="no">No, use element identifiers as is</option>\n@@ -969,7 +970,7 @@\n <option value="individual">Associate individual files</option>\n </param>\n <when value="collection">\n- <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: .+_.+_L[0-9][0-9][0-9]_R[12]_001\\.fastq\\.gz"/>\n+ <param name="elements" type="data_collection" collection_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9'..b'ion_type="list" help="This data should be formatted as a FastqGzFormat. See the documentation below for more information. Elements must match regex: .+_.+_L[0-9][0-9][0-9]_R[12]_001\\.fastq\\.gz"/>\n <conditional name="__q2galaxy__GUI__cond__add_ext__">\n <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one.">\n <option value="no">No, use element identifiers as is</option>\n@@ -1657,6 +1658,64 @@\n <outputs>\n <data name="imported_data" format="qza" from_work_dir="imported_data.qza"/>\n </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="import_root">\n+ <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>\n+ <conditional name="__q2galaxy__GUI__cond__format__">\n+ <param name="format" value="CasavaOneEightLanelessPerSampleDirFmt"/>\n+ <section name="import_sequences">\n+ <conditional name="__q2galaxy__GUI__cond__sequences__">\n+ <param name="__q2galaxy__GUI__select__picker__" value="collection"/>\n+ <param name="elements">\n+ <collection type="list">\n+ <element name="YY_S49_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />\n+ <element name="YY_S49_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />\n+ </collection>\n+ </param>\n+ <conditional name="__q2galaxy__GUI__cond__add_ext__">\n+ <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>\n+ <param name="ext" label="fastq.gz"/>\n+ </conditional>\n+ </conditional>\n+ </section>\n+ </conditional>\n+ </conditional>\n+ <output name="imported_data">\n+ <assert_contents>\n+ <has_size min="1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="import_root">\n+ <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/>\n+ <conditional name="__q2galaxy__GUI__cond__format__">\n+ <param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/>\n+ <section name="import_sequences">\n+ <conditional name="__q2galaxy__GUI__cond__sequences__">\n+ <param name="__q2galaxy__GUI__select__picker__" value="collection"/>\n+ <param name="elements">\n+ <collection type="list">\n+ <element name="YY_S49_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" />\n+ <element name="YY_S49_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" />\n+ </collection>\n+ </param>\n+ <conditional name="__q2galaxy__GUI__cond__add_ext__">\n+ <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/>\n+ <param name="ext" label="fastq.gz"/>\n+ </conditional>\n+ </conditional>\n+ </section>\n+ </conditional>\n+ </conditional>\n+ <output name="imported_data">\n+ <assert_contents>\n+ <has_size min="1"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n <help>\n QIIME 2: tools import\n =====================\n' |
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