Mercurial > repos > q2d2 > qiime2_core__tools__import
changeset 3:10447a4b0cc3 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools commit db44258c63cb7e98d605a94464066fc8a5ef75ac
| author | q2d2 |
|---|---|
| date | Thu, 01 Feb 2024 21:22:08 +0000 |
| parents | 18c6b2b6740f |
| children | 9dbdf05beaa9 |
| files | qiime2_core__tools__import.xml test-data/YY/YY_S49_R1_001.fastq.gz test-data/YY/YY_S49_R2_001.fastq.gz |
| diffstat | 3 files changed, 76 insertions(+), 17 deletions(-) [+] |
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--- 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 @@ -10,7 +10,7 @@ for: qiime2 (version: 2023.5.1) --> -<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 tools import" id="qiime2_core__tools__import" version="2023.5.0+dist.h193f7cc9.3" profile="22.05" license="BSD-3-Clause"> <description>Import data into a QIIME 2 artifact</description> <requirements> <container type="docker">quay.io/qiime2/core:2023.5</container> @@ -20,6 +20,7 @@ <configfile name="inputs"><% # This is an exercise in cheating the Cheetah import json +from collections.abc import MutableMapping def expand_collection(collection): # All of this work is just to extract the @@ -28,7 +29,7 @@ for d in collection] def stringify(obj): - if type(obj) is dict: + if isinstance(obj, MutableMapping): new = {} for key, value in obj.items(): if (key.startswith('__') and key.endswith('__') @@ -357,7 +358,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -938,7 +939,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -969,7 +970,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1000,7 +1001,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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: .+\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1055,7 +1056,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1094,7 +1095,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1146,7 +1147,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1177,7 +1178,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1232,7 +1233,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1312,7 +1313,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1343,7 +1344,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1374,7 +1375,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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: .+\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1429,7 +1430,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1468,7 +1469,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1521,7 +1522,7 @@ <option value="individual">Associate individual files</option> </param> <when value="collection"> - <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"/> + <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][0-9]_R[12]_001\.fastq\.gz"/> <conditional name="__q2galaxy__GUI__cond__add_ext__"> <param name="__q2galaxy__GUI__select__ext_pick__" type="select" label="Append an extension?" help="This is needed if your element identifiers lack one."> <option value="no">No, use element identifiers as is</option> @@ -1657,6 +1658,64 @@ <outputs> <data name="imported_data" format="qza" from_work_dir="imported_data.qza"/> </outputs> + <tests> + <test> + <conditional name="import_root"> + <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" value="CasavaOneEightLanelessPerSampleDirFmt"/> + <section name="import_sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <param name="__q2galaxy__GUI__select__picker__" value="collection"/> + <param name="elements"> + <collection type="list"> + <element name="YY_S49_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" /> + <element name="YY_S49_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" /> + </collection> + </param> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/> + <param name="ext" label="fastq.gz"/> + </conditional> + </conditional> + </section> + </conditional> + </conditional> + <output name="imported_data"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </output> + </test> + <test> + <conditional name="import_root"> + <param name="type" value="SampleData__ob__PairedEndSequencesWithQuality__cb__"/> + <conditional name="__q2galaxy__GUI__cond__format__"> + <param name="format" value="CasavaOneEightSingleLanePerSampleDirFmt"/> + <section name="import_sequences"> + <conditional name="__q2galaxy__GUI__cond__sequences__"> + <param name="__q2galaxy__GUI__select__picker__" value="collection"/> + <param name="elements"> + <collection type="list"> + <element name="YY_S49_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R1_001.fastq.gz" /> + <element name="YY_S49_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" value="YY/YY_S49_R2_001.fastq.gz" /> + </collection> + </param> + <conditional name="__q2galaxy__GUI__cond__add_ext__"> + <param name="__q2galaxy__GUI__select__ext_pick__" value="yes"/> + <param name="ext" label="fastq.gz"/> + </conditional> + </conditional> + </section> + </conditional> + </conditional> + <output name="imported_data"> + <assert_contents> + <has_size min="1"/> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: tools import =====================