| Previous changeset 0:1c664ff29354 (2020-05-04) Next changeset 2:2e993ff8e7dc (2021-11-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb" |
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modified:
sarscov2formatter.xml test-data/dups.json |
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added:
test-data/test.py test-data/test.tsv |
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removed:
test-data/meta.json |
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| diff -r 1c664ff29354 -r e3a7995dce75 sarscov2formatter.xml --- a/sarscov2formatter.xml Mon May 04 05:39:35 2020 -0400 +++ b/sarscov2formatter.xml Fri Nov 20 18:21:33 2020 +0000 |
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| @@ -1,10 +1,10 @@ -<tool id="sarscov2formatter" name="sarscov2formatter" version="0.1" profile="18.01"> +<tool id="sarscov2formatter" name="sarscov2formatter" version="0.5.3+galaxy1" profile="18.01"> <requirements> - <requirement type="package" version="0.5.2">sarscov2formatter</requirement> + <requirement type="package" version="0.5.3">sarscov2formatter</requirement> </requirements> <command><![CDATA[ sarscov2formatter --a $align +-a '$align' #if $source.source_choice == 'ncbi': -m ncbi #else: @@ -20,7 +20,7 @@ </param> <when value="ncbi" /> <when value="other" > - <param name="meta" type="data" format='tabular' label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" /> + <param name="meta" type="data" format="tabular" label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" /> </when> </conditional> </inputs> @@ -30,13 +30,42 @@ <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" /> </outputs> <tests> + <!-- note: test with ncbi yields unstable results for meta -> assert contents. + also needs a surprising amount memory (1.7G) which might + become impractival in the future --> <test> <param name="align" ftype="fasta" value="align.fasta" /> <param name="source_choice" value="ncbi" /> <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" /> <output name="dups" ftype="json" compare="diff" value="dups.json" /> - <output name="outmeta" ftype="json" compare="diff" value="meta.json" /> + <output name="outmeta" ftype="json"> + <assert_contents> + <has_line_matching expression="\{"/> + <has_line_matching expression="\}"/> + <has_text_matching expression='"LR757995": \{'/> + <has_text_matching expression='"collected": '/> + <has_text_matching expression='"collected": '/> + <has_text_matching expression='"location": '/> + <has_text_matching expression='"country": '/> + <has_text_matching expression='"locality": '/> + <has_text_matching expression='"state": '/> + <has_text_matching expression='"subregion": '/> + </assert_contents> + </output> </test> + <!-- TODO test with tabular input, does not work yet + test.tsv has been generated with test.py + https://github.com/nickeener/sarscov2formatter/issues/2 --> +<!-- <test>--> +<!-- <param name="align" ftype="fasta" value="align.fasta" />--> +<!-- <conditional name="source" >--> +<!-- <param name="source_choice" value="other" />--> +<!-- <param name="meta" ftype="tabular" value="test.tsv" />--> +<!-- </conditional>--> +<!-- <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />--> +<!-- <output name="dups" ftype="json" compare="diff" value="dups-other.json" />--> +<!-- <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />--> +<!-- </test>--> </tests> <help><![CDATA[ |
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| diff -r 1c664ff29354 -r e3a7995dce75 test-data/dups.json --- a/test-data/dups.json Mon May 04 05:39:35 2020 -0400 +++ b/test-data/dups.json Fri Nov 20 18:21:33 2020 +0000 |
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| @@ -1,1 +1,68 @@ -{"MultiSeq0_24": {"1": "MT019530", "2": "MT027062", "3": "MT159705", "4": "MT159710", "5": "MT192773", "6": "MT240479", "7": "MT246472", "8": "MT253699", "9": "MT259275", "10": "MT262910", "11": "MT262912", "12": "MT263399", "13": "MT263435", "14": "MT263451", "15": "MT304482", "16": "MT304483", "17": "MT326151", "18": "MT325578", "19": "MT325609", "20": "MT334533", "21": "MT334534", "22": "MT350276"}, "MultiSeq1_15": {"1": "MT276327", "2": "MT293173", "3": "MT293195", "4": "MT326113", "5": "MT326162", "6": "MT326189", "7": "MT325626", "8": "MT345825", "9": "MT345827", "10": "MT345834", "11": "MT345835", "12": "MT345857", "13": "MT344957"}, "MT350282": {"0": "MT350282"}, "MT345866": {"0": "MT345866"}, "MT293207": {"0": "MT293207"}, "MT292573": {"0": "MT292573"}, "MT292570": {"0": "MT292570"}, "MT263469": {"0": "MT263469"}, "MT263450": {"0": "MT263450"}, "MT263436": {"0": "MT263436"}, "MN988713": {"0": "MN988713"}} \ No newline at end of file +{ + "MN988713": { + "0": "MN988713" + }, + "MT263436": { + "0": "MT263436" + }, + "MT263450": { + "0": "MT263450" + }, + "MT263469": { + "0": "MT263469" + }, + "MT292570": { + "0": "MT292570" + }, + "MT292573": { + "0": "MT292573" + }, + "MT293207": { + "0": "MT293207" + }, + "MT345866": { + "0": "MT345866" + }, + "MT350282": { + "0": "MT350282" + }, + "MultiSeq0_24": { + "1": "MT019530", + "10": "MT262910", + "11": "MT262912", + "12": "MT263399", + "13": "MT263435", + "14": "MT263451", + "15": "MT304482", + "16": "MT304483", + "17": "MT326151", + "18": "MT325578", + "19": "MT325609", + "2": "MT027062", + "20": "MT334533", + "21": "MT334534", + "22": "MT350276", + "3": "MT159705", + "4": "MT159710", + "5": "MT192773", + "6": "MT240479", + "7": "MT246472", + "8": "MT253699", + "9": "MT259275" + }, + "MultiSeq1_15": { + "1": "MT276327", + "10": "MT345834", + "11": "MT345835", + "12": "MT345857", + "13": "MT344957", + "2": "MT293173", + "3": "MT293195", + "4": "MT326113", + "5": "MT326162", + "6": "MT326189", + "7": "MT325626", + "8": "MT345825", + "9": "MT345827" + } +} \ No newline at end of file |
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| diff -r 1c664ff29354 -r e3a7995dce75 test-data/meta.json --- a/test-data/meta.json Mon May 04 05:39:35 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"NC_045512": {"collected": "20200117", "location": {"subregion": "Asia", "country": "China", "state": null, "locality": null}}, "MT350282": {"collected": "20200318", "location": {"subregion": "South America", "country": "Brazil", "state": null, "locality": null}}, "MT350276": {"collected": "20200319", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT345866": {"collected": "20200323", "location": {"subregion": "North America", "country": "USA", "state": "ID", "locality": null}}, "MT345857": {"collected": "20200324", "location": {"subregion": "North America", "country": "USA", "state": "ID", "locality": null}}, "MT345835": {"collected": "20200325", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT345834": {"collected": "20200326", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT345827": {"collected": "20200325", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT345825": {"collected": "20200325", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT344957": {"collected": "20200307", "location": {"subregion": "North America", "country": "USA", "state": "PA", "locality": null}}, "MT334534": {"collected": "20200313", "location": {"subregion": "North America", "country": "USA", "state": "UT", "locality": null}}, "MT334533": {"collected": "20200313", "location": {"subregion": "North America", "country": "USA", "state": "UT", "locality": null}}, "MT326189": {"collected": "20200318", "location": {"subregion": "North America", "country": "USA", "state": null, "locality": null}}, "MT326162": {"collected": "20200321", "location": {"subregion": "North America", "country": "USA", "state": null, "locality": null}}, "MT326151": {"collected": "20200321", "location": {"subregion": "North America", "country": "USA", "state": null, "locality": null}}, "MT326113": {"collected": "20200320", "location": {"subregion": "North America", "country": "USA", "state": null, "locality": null}}, "MT325626": {"collected": "20200305", "location": {"subregion": "North America", "country": "USA", "state": "SC", "locality": null}}, "MT325609": {"collected": "20200305", "location": {"subregion": "North America", "country": "USA", "state": "UT", "locality": null}}, "MT325578": {"collected": "20200307", "location": {"subregion": "North America", "country": "USA", "state": "IL", "locality": null}}, "MT304483": {"collected": "20200301", "location": {"subregion": "North America", "country": "USA", "state": "IL", "locality": null}}, "MT304482": {"collected": "20200301", "location": {"subregion": "North America", "country": "USA", "state": "IL", "locality": null}}, "MT293207": {"collected": "20200319", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT293195": {"collected": "20200328", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT293173": {"collected": "20200330", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT292573": {"collected": "20200309", "location": {"subregion": "Europe", "country": "Spain", "state": null, "locality": null}}, "MT292570": {"collected": "20200310", "location": {"subregion": "Europe", "country": "Spain", "state": null, "locality": null}}, "MT276327": {"collected": "20200229", "location": {"subregion": "North America", "country": "USA", "state": "GA", "locality": null}}, "MT263469": {"collected": "20200315", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT263467": {"collected": "20200316", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT263451": {"collected": "20200316", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT263450": {"collected": "20200324", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT263436": {"collected": "20200324", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT263435": {"collected": "20200324", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT263399": {"collected": "20200324", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT262912": {"collected": "20200313", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT262910": {"collected": "20200313", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT259275": {"collected": "20200314", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT253699": {"collected": "20200124", "location": {"subregion": "Asia", "country": "China", "state": "Zhejiang", "locality": "Hangzhou"}}, "MT246472": {"collected": "20200312", "location": {"subregion": "North America", "country": "USA", "state": "WA", "locality": null}}, "MT240479": {"collected": "20200304", "location": {"subregion": "Asia", "country": "Pakistan", "state": "Gilgit", "locality": null}}, "MT192773": {"collected": "20200122", "location": {"subregion": "Asia", "country": "Vietnam", "state": "Ho Chi Minh city", "locality": null}}, "MT159710": {"collected": "20200217", "location": {"subregion": "North America", "country": "USA", "state": null, "locality": null}}, "MT159705": {"collected": "20200217", "location": {"subregion": "North America", "country": "USA", "state": null, "locality": null}}, "MT027062": {"collected": "20200129", "location": {"subregion": "North America", "country": "USA", "state": "CA", "locality": null}}, "MT019530": {"collected": "20191230", "location": {"subregion": "Asia", "country": "China", "state": "Hubei", "locality": "Wuhan"}}, "MN988713": {"collected": "20200121", "location": {"subregion": "North America", "country": "USA", "state": "Illinois", "locality": null}}, "LR757995": {"collected": "20191226", "location": {"subregion": "Asia", "country": "China", "state": "uhan", "locality": null}}} \ No newline at end of file |
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| diff -r 1c664ff29354 -r e3a7995dce75 test-data/test.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.py Fri Nov 20 18:21:33 2020 +0000 |
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| @@ -0,0 +1,10 @@ +import json + +with open("meta.json") as jh: + data = json.load(jh) + +print("ID\tcollection_date\tcountry\tstate\tlocality") +for k in data: + collection_date = data[k]['collected'] + location = data[k]['location'] + print("%s\t%s\t%s\t%s\t%s" % (k, collection_date, location['country'], location['state'], location['locality'])) |
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| diff -r 1c664ff29354 -r e3a7995dce75 test-data/test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tsv Fri Nov 20 18:21:33 2020 +0000 |
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| @@ -0,0 +1,48 @@ +ID collection_date country state locality +LR757995 20191226 China uhan None +MT027062 20200129 USA CA None +MT325626 20200305 USA SC None +MT325609 20200305 USA UT None +MT263436 20200324 USA WA None +MT263435 20200324 USA WA None +MT326162 20200321 USA None None +MT159710 20200217 USA None None +MT259275 20200314 USA WA None +MT325578 20200307 USA IL None +MT276327 20200229 USA GA None +MT345866 20200323 USA ID None +MT345857 20200324 USA ID None +MT192773 20200122 Vietnam Ho Chi Minh city None +MT304482 20200301 USA IL None +MT304483 20200301 USA IL None +MT292573 20200309 Spain None None +MT246472 20200312 USA WA None +MT345835 20200325 USA WA None +MT293195 20200328 USA WA None +MT345827 20200325 USA WA None +MT344957 20200307 USA PA None +MT293173 20200330 USA WA None +NC_045512 20200117 China None None +MT263467 20200316 USA WA None +MT345825 20200325 USA WA None +MT350282 20200318 Brazil None None +MT263469 20200315 USA WA None +MT263399 20200324 USA WA None +MT326113 20200320 USA None None +MT159705 20200217 USA None None +MT326151 20200321 USA None None +MN988713 20200121 USA Illinois None +MT019530 20191230 China Hubei Wuhan +MT350276 20200319 USA WA None +MT240479 20200304 Pakistan Gilgit None +MT253699 20200124 China Zhejiang Hangzhou +MT292570 20200310 Spain None None +MT345834 20200326 USA WA None +MT293207 20200319 USA WA None +MT262912 20200313 USA WA None +MT326189 20200318 USA None None +MT262910 20200313 USA WA None +MT334534 20200313 USA UT None +MT263451 20200316 USA WA None +MT263450 20200324 USA WA None +MT334533 20200313 USA UT None |