Mercurial > repos > iuc > ncbi_datasets

annotate datasets_genome.xml @ 15:198c75abbf55 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
author iuc
date Mon, 04 Mar 2024 17:27:59 +0000
parents 75acf92c8fd5
children a6a475ed58cb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
0622d99c2619 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 7fc0becfda6c41c95d4aa9ee32ae0539be9b6210
iuc
parents: 6
diff changeset
1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
2 <description>download genome sequence, annotation and metadata</description>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
3 <macros>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
5 </macros>
13
1e188c9610c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9
iuc
parents: 12
diff changeset
6 <expand macro="bio_tools"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
7 <expand macro="requirements"></expand>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
8 <expand macro="version_command"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
9 <command><![CDATA[
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
10 #import re
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
11 @SETUP_CERTIFICATES@
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
12 datasets download genome $query.subcommand.download_by
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
13 #if $query.subcommand.download_by == 'accession':
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
14 #if $query.subcommand.text_or_file.text_or_file == 'text':
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
15 #echo " ".join(f"'{x}'" for x in re.split(" |,", str($query.subcommand.text_or_file.accession)) if x)
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
16 #else
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
17 --inputfile '$query.subcommand.text_or_file.inputfile'
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
18 #end if
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
19 #else:
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
20 '$query.subcommand.taxon_positional'
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
21 $query.subcommand.tax_exact_match
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
22 #end if
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
23 $filters.reference
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
24 $filters.annotated
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
25 #if $filters.assembly_level:
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
26 --assembly-level $filters.assembly_level
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
27 #end if
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
28 --assembly-version $filters.assembly_version
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
29 #if $filters.assembly_source:
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
30 --assembly-source $filters.assembly_source
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
31 #end if
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
32 #if $filters.chromosomes:
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
33 --chromosomes '$filters.chromosomes'
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
34 #end if
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
35 $filters.exclude_atypical
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
36 #if $filters.mag:
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
37 --mag '$filters.mag'
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
38 #end if
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
39
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
40 @INCLUDE@
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
41 @RELEASED_BEFORE@
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
42 @RELEASED_AFTER@
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
43 #for search_term in $filters.search:
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
44 --search '$filters.search_term'
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
45 #end for
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
46 --no-progressbar
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
47 --dehydrated
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
48
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
49 ## produce TSV report file
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
50 && dataformat tsv genome
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
51 --package ncbi_dataset.zip
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
52 --fields #echo ",".join($file_choices.report_columns)
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
53 > genome_data_report.tsv
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
54
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
55 ## unzip and rehydrate if any data is to be downloaded (include is not None)
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
56 #if $file_choices.include
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
57 ## unzip
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
58 && 7z x -y ncbi_dataset.zip > 7z.log
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
59
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
60 ## rehydrate
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
61 && datasets rehydrate
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
62 --directory ./
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
63 #if not $file_choices.decompress
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
64 --gzip
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
65 #end if
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
66 --max-workers \${NCBI_DATASETS_MAX_WORKERS:-10}
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
67
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
68 ## rename all faa, fna (resp faa.gz, fna.gz) to fasta (resp fasta.gz) to allow discovery
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
69 && find ncbi_dataset \( -name "*.faa" -o -name "*.fna" -o -name "*.faa.gz" -o -name "*.fna.gz" \) -exec sh -c 'mv {} \$(echo {} | sed "s/.f[an]a\(.gz\)\?\$/.fasta\1/")' \;
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
70
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
71 ## unzip all compressed (non-fasta) files (jsonl files are just named .gz)
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
72 ## note "not decompress" means that the datasets are provided uncompressed (datasets rehydrate is called we --gzip)
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
73 ## in this case we need to decompress all datasets that don't have a Galaxy datatype allowing for compression
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
74 && find ncbi_dataset -name "*.jsonl.gz" -exec sh -c 'mv {} \$(dirname {})/\$(basename {} .gz)' \;
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
75 #if not $file_choices.decompress
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
76 && find ncbi_dataset \( -name "*.gz" ! -name "*fasta.gz" \) -exec gunzip {} \;
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
77 #end if
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
78
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
79 #if "seq-report" in $file_choices.include
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
80 && find ncbi_dataset -name sequence_report.jsonl -exec sh -c 'dataformat tsv genome-seq --inputfile {} > \$(dirname {})/\$(basename {} .jsonl).tsv' \;
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
81 #end if
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
82
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
83 && true ## because Galaxy removes trailing ; from command
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
84 #end if
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
85 ]]></command>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
86 <inputs>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
87 <section name="query" title="Query" expanded="true">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
88 <conditional name="subcommand">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
89 <param name="download_by" type="select" label="Choose how to find genomes to download">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
90 <option value="accession">By NCBI assembly or BioProject accession</option>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
91 <option value="taxon">By taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)</option>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
92 </param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
93 <when value="accession">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
94 <expand macro="text_or_file"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
95 </when>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
96 <when value="taxon">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
97 <expand macro="taxon_positional"/>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
98 <param argument="--tax-exact-match" type="boolean" truevalue="--tax-exact-match" falsevalue="" label="Exclude sub-species when a species-level taxon is specified"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
99 </when>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
100 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
101 </section>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
102 <section name="filters" title="Filters and Limit">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
103 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
104 <expand macro="annotation"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
105 <expand macro="assembly_level"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
106 <param argument="--assembly-version" type="select" label="Assembly version(s)">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
107 <option value="latest">Latest</option>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
108 <option value="all">All</option>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
109 </param>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
110 <expand macro="assembly_source"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
111 <expand macro="chromosomes"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
112 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
113 <param argument="--mag" type="select" multiple="false" optional="true" label="Filter metagenome assembled genomes (MAGs)">
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
114 <option value="only" selected="false">Limit to MAGs</option>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
115 <option value="exclude" selected="false">Exclude MAGs</option>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
116 </param>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
117 <expand macro="released_options"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
118 <expand macro="released_options" before_or_after="after"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
119
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
120 <repeat name="search" title="Add search terms">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
121 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
122 </repeat>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
123 </section>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
124 <section name="file_choices" title="Output options" expanded="true">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
125 <expand macro="tsv_report_columns">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
126 <option value="accession" selected="true">accession</option>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
127 <option value="organism-name" selected="true">organism-name</option>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
128 <option value="assminfo-submitter" selected="true">assminfo-submitter</option>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
129 <option value="assminfo-name" selected="true">assminfo-name</option>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
130 </expand>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
131 <expand macro="include">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
132 <expand macro="genome_includes"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
133 </expand>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
134 <param name="decompress" type="boolean" label="Decompress FASTA" help="By default FASTA files are provided zipped (fasta.gz) if this is checked the data will be decompressed"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
135 </section>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
136 </inputs>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
137 <outputs>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
138 <data name="genome_data_report" format="tabular" label="NCBI Genome Datasets: Data Report" from_work_dir="genome_data_report.tsv"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
139 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
140 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.tsv" ext="tabular" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
141 <filter>file_choices['include'] and "seq-report" in file_choices['include']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
142 </collection>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
143 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
144 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)(_genomic)?\.(?P&lt;ext&gt;fasta(\.gz)?)" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
145 <filter>file_choices['include'] and "genome" in file_choices['include']</filter>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
146 </collection>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
147 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
148 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.(?P&lt;ext&gt;fasta(\.gz)?)$" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
149 <filter>file_choices['include'] and "rna" in file_choices['include']</filter>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
150 </collection>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
151 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
152 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.(?P&lt;ext&gt;fasta(\.gz)?)$" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
153 <filter>file_choices['include'] and "protein" in file_choices['include']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
154 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
155 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
156 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.(?P&lt;ext&gt;fasta(\.gz)?)$" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
157 <filter>file_choices['include'] and "cds" in file_choices['include']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
158 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
159 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
160 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
161 <filter>file_choices['include'] and "gff3" in file_choices['include']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
162 </collection>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
163 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
164 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
165 <filter>file_choices['include'] and "gtf" in file_choices['include']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
166 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
167 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
168 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
169 <filter>file_choices['include'] and "gbff" in file_choices['include']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
170 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
171 </outputs>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
172 <tests>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
173 <test expect_num_outputs="3">
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
174 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
175 <param name="download_by" value="taxon"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
176 <param name="taxon_positional" value="human"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
177 </conditional>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
178 <param name="chromosomes" value="21"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
179 <param name="released_before" value="01/01/2018"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
180 <section name="file_choices">
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
181 <!-- include a sequence (which should be downloaded as fasta.gz)
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
182 and one non-sequence (which should be decompressed) output -->
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
183 <param name="include" value="rna,gff3"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
184 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
185 <output name="genome_data_report">
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
186 <assert_contents>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
187 <has_text text="Assembly Accession&#009;Assembly Name&#009;Assembly Submitter&#009;Organism Name"/>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
188 <has_n_lines n="142"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
189 <has_n_columns n="4"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
190 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
191 </output>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
192 <output_collection name="rna_fasta" type="list" count="1">
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
193 <element name="GCF_000306695.2" decompress="true">
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
194 <assert_contents>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
195 <has_text text=">"/>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
196 </assert_contents>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
197 </element>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
198 </output_collection>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
199 <output_collection name="genomic_gff" type="list">
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
200 <element name="GCF_000306695.2">
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
201 <assert_contents>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
202 <has_n_lines min="1000000"/>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
203 <has_line line="##gff-version 3"/>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
204 <has_n_columns n="9" comment="#"/>
12
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
205 </assert_contents>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
206 </element>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
207 </output_collection>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
208 <assert_command>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
209 <has_text text="gunzip"/>
d78faac2c6ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit affffdbe7237a2c0ba5793c0e7dd11cebb8413a9
iuc
parents: 11
diff changeset
210 </assert_command>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
211 </test>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
212 <test expect_num_outputs="2">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
213 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
214 <param name="download_by" value="taxon"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
215 <param name="taxon_positional" value="human"/>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
216 </conditional>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
217 <param name="chromosomes" value="21"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
218 <param name="assembly_level" value="chromosome,complete"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
219 <param name="released_before" value="01/01/2018"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
220 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
221 <param name="include" value="genome"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
222 <param name="decompress" value="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
223 </section>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
224 <output_collection name="genome_fasta" type="list:list" count="12">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
225 <expand macro="genome_fasta_assert" el1="GCA_000002115.2" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
226 <expand macro="genome_fasta_assert" el1="GCA_000002125.2" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
227 <expand macro="genome_fasta_assert" el1="GCA_000212995.1" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
228 <expand macro="genome_fasta_assert" el1="GCA_000252825.1" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
229 <expand macro="genome_fasta_assert" el1="GCA_000306695.2" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
230 <expand macro="genome_fasta_assert" el1="GCA_000365445.1" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
231 <expand macro="genome_fasta_assert" el1="GCA_001292825.2" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
232 <expand macro="genome_fasta_assert" el1="GCA_001524155.4" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
233 <expand macro="genome_fasta_assert" el1="GCA_001712695.1" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
234 <expand macro="genome_fasta_assert" el1="GCA_022833125.2" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
235 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
236 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
237 <!-- According to https://github.com/ncbi/datasets/issues/188, the following should not be included among the returned results anymore 09/2023 -->
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
238 <!--
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
239 <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/>
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
240 <expand macro="genome_fasta_assert" el1="GCA_000002135.3" el2="GCA_000002135.3_CRA_TCAGchr7v2" expression=">"/>
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
241 -->
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
242 </output_collection>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
243 <output name="genome_data_report">
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
244 <assert_contents>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
245 <has_text text="Homo sapiens"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
246 <has_n_columns n="4"/>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
247 </assert_contents>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
248 </output>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
249 </test>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
250 <!-- same as previous test but assembly_source=refseq, which removes all of the genomes -->
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
251 <test expect_failure="true">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
252 <conditional name="query|subcommand">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
253 <param name="download_by" value="taxon"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
254 <param name="taxon_positional" value="human"/>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
255 </conditional>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
256 <param name="chromosomes" value="21"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
257 <param name="assembly_level" value="chromosome,complete"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
258 <param name="assembly_source" value="refseq"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
259 <param name="released_before" value="01/01/2018"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
260 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
261 <param name="include" value="genome"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
262 <param name="decompress" value="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
263 </section>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
264 <assert_stderr>
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
265 <has_text text="No assemblies found that match selection"/>
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
266 </assert_stderr>
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
267 <!-- In the current state of the NCBI tool/DB, no output to check.
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
268 But the returned results seem to change from time to time and it might
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
269 be necessary to re-enable this code block if the test fails in the future. -->
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
270 <!--
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
271 <output_collection name="genome_fasta" type="list:list" count="2">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
272 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
273 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
274 </output_collection>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
275 <output name="genome_data_report">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
276 <assert_contents>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
277 <has_text text="Homo sapiens"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
278 <has_n_lines n="5"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
279 <has_n_columns n="4"/>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
280 </assert_contents>
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
281 </output> -->
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
282 </test>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
283 <test expect_num_outputs="4">
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
284 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
285 <param name="download_by" value="accession"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
286 <conditional name="text_or_file">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
287 <param name="text_or_file" value="text"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
288 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
289 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
290 </conditional>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
291 <param name="released_before" value="01/01/2007"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
292 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
293 <param name="include" value="seq-report,gtf,cds"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
294 <param name="decompress" value="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
295 </section>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
296 <output name="genome_data_report">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
297 <assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
298 <has_text text="GCF_000013305.1"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
299 <has_n_lines n="3"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
300 <has_n_columns n="4"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
301 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
302 </output>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
303 <output_collection name="sequence_report" type="list" count="2" >
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
304 <element name="GCF_000007445.1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
305 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
306 <has_text text="GCF_000007445.1"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
307 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
308 <has_n_columns n="14"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
309 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
310 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
311 <element name="GCF_000013305.1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
312 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
313 <has_text text="GCF_000013305.1"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
314 <has_n_lines n="2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
315 <has_n_columns n="14"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
316 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
317 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
318 </output_collection>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
319 <output_collection name="genomic_gtf" type="list">
9
18eed8fa7f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit baddca770f8ae8475785374d883b3b42fac27c0c
iuc
parents: 8
diff changeset
320 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
321 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
322 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
323 <output_collection name="genomic_cds" type="list">
14
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
324 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/>
75acf92c8fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39
iuc
parents: 13
diff changeset
325 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
326 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
327 </test>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
328 <test expect_num_outputs="4">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
329 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
330 <param name="download_by" value="accession"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
331 <conditional name="text_or_file">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
332 <param name="text_or_file" value="file"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
333 <param name="inputfile" value="accessions.txt"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
334 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
335 </conditional>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
336 <param name="released_before" value="01/01/2007"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
337 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
338 <param name="include" value="seq-report,gff3,gbff"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
339 <param name="decompress" value="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
340 </section>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
341 <output name="genome_data_report">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
342 <assert_contents>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
343 <has_text text="GCF_000013305.1"/>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
344 <has_text text="GCF_000007445.1"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
345 <has_n_lines n="3"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
346 <has_n_columns n="4"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
347 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
348 </output>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
349 <output_collection name="genomic_gff" type="list">
9
18eed8fa7f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit baddca770f8ae8475785374d883b3b42fac27c0c
iuc
parents: 8
diff changeset
350 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
351 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
352 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
353 <output_collection name="genomic_gbff" type="list">
9
18eed8fa7f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit baddca770f8ae8475785374d883b3b42fac27c0c
iuc
parents: 8
diff changeset
354 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
355 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
356 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
357 </test>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
358
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
359 <!-- should not fail https://github.com/ncbi/datasets/issues/194 -->
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
360 <test expect_num_outputs="2">
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
361 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
362 <param name="download_by" value="accession"/>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
363 <conditional name="text_or_file">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
364 <param name="text_or_file" value="text"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
365 <param name="accession" value="GCF_000001405"/>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
366 </conditional>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
367 </conditional>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
368 <param name="released_before" value="01/01/2015"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
369 <param name="assembly_version" value="all"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
370 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
371 <param name="include" value="seq-report"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
372 </section>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
373 <output name="genome_data_report">
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
374 <!-- assert that we get at least the 16 versions available at the time of writing this test -->
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
375 <assert_contents>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
376 <has_text text="GCF_000001405" min="16"/>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
377 <has_n_lines min="16"/>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
378 <has_n_columns n="4"/>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
379 </assert_contents>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
380 </output>
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
381 <!--not testing the collection output. the count will change over time
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
382 and this can't be tested for at the moment
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
383 <output_collection name="sequence_report" type="list" count="16"/> -->
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
384 </test>
7
0622d99c2619 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 7fc0becfda6c41c95d4aa9ee32ae0539be9b6210
iuc
parents: 6
diff changeset
385 <test expect_num_outputs="5">
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
386 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
387 <param name="download_by" value="accession"/>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
388 <conditional name="text_or_file">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
389 <param name="text_or_file" value="text"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
390 <param name="accession" value="GCF_000146045.2"/>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
391 </conditional>
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
392 </conditional>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
393 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
394 <param name="include" value="genome,protein,rna,cds"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
395 <param name="decompress" value="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
396 </section>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
397 <output_collection name="genome_fasta" type="list:list" count="1">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
398 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
399 </output_collection>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
400 <output_collection name="protein_fasta" type="list" count="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
401 <element name="GCF_000146045.2" decompress="true">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
402 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
403 <has_text text=">"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
404 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
405 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
406 </output_collection>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
407 <output_collection name="rna_fasta" type="list" count="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
408 <element name="GCF_000146045.2" decompress="true">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
409 <assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
410 <has_text text=">"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
411 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
412 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
413 </output_collection>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
414 </test>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
415 <!-- same as the previous test, but use the default value for decompress,
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
416 see comment at the beginning of the tests -->
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
417 <test expect_num_outputs="5">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
418 <conditional name="query|subcommand">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
419 <param name="download_by" value="accession"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
420 <conditional name="text_or_file">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
421 <param name="text_or_file" value="text"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
422 <param name="accession" value="GCF_000146045.2"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
423 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
424 </conditional>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
425 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
426 <param name="include" value="genome,protein,rna,cds"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
427 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
428 <output_collection name="genome_fasta" type="list:list" count="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
429 <element name="GCF_000146045.2">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
430 <element name="GCF_000146045.2_R64" ftype="fasta.gz">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
431 <assert_contents>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
432 <has_size value="3843460" delta="2000"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
433 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
434 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
435 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
436 </output_collection>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
437 <output_collection name="protein_fasta" type="list" count="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
438 <element name="GCF_000146045.2" ftype="fasta.gz">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
439 <assert_contents>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
440 <has_size value="1845038" delta="2000"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
441 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
442 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
443 </output_collection>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
444 <output_collection name="rna_fasta" type="list" count="1">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
445 <element name="GCF_000146045.2" ftype="fasta.gz">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
446 <assert_contents>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
447 <has_size value="2784899" delta="2000"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
448 </assert_contents>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
449 </element>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
450 </output_collection>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
451 </test>
8
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
452 <test expect_num_outputs="3">
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
453 <conditional name="query|subcommand">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
454 <param name="download_by" value="accession"/>
8
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
455 <conditional name="text_or_file">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
456 <param name="text_or_file" value="text"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
457 <param name="accession" value="GCF_000146045.2 GCF_000002945.1"/>
8
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
458 </conditional>
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
459 </conditional>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
460 <section name="file_choices">
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
461 <param name="include" value="seq-report,genome"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
462 <param name="decompress" value="true"/>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
463 </section>
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
464 <output_collection name="sequence_report" type="list" count="2"/>
8
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
465 <output_collection name="genome_fasta" type="list:list" count="2">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
466 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
467 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
8
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
468 </output_collection>
b2ae7186d41f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
iuc
parents: 7
diff changeset
469 </test>
15
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
470 <!-- tax_exact_match should filter out strains
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
471 https://github.com/ncbi/datasets/issues/187 -->
198c75abbf55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1b6341a0430757c07760af2115ae4d5e70f5903a
iuc
parents: 14
diff changeset
472 <test expect_num_outputs="1">
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
473 <conditional name="query|subcommand">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
474 <param name="download_by" value="taxon"/>
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
475 <param name="taxon_positional" value="4932"/>
10
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
476 <param name="tax_exact_match" value="true"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
477 </conditional>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
478 <param name="include" value=""/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
479 <output name="genome_data_report">
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
480 <assert_contents>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
481 <has_text text="Saccharomyces cerevisiae ZTW1" negate="true"/>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
482 </assert_contents>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
483 </output>
a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
iuc
parents: 9
diff changeset
484 </test>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
485 </tests>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
486 <help>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
487 <![CDATA[
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
488 **Download Genome Datasets from NCBI**
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
489
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
490 Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report.
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
491 Genome datasets can be specified by NCBI Assembly or BioProject accession(s) or by taxon.
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
492
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
493 The download is a three step process:
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
494
11
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
495 1. A "dehydrated" zip file is downloaded which includes the metadata and the download URL)
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
496 2. The metadata is transformed into a tabular (TSV) file
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
497 3. The data is hydrated (the actual data is downloaded)
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
498
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
499 The 3rd step can be skipped by unselecting all output types in the `Include` parameter.
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
500 Thereby its possible to inspect the metadata prior to the actual data download. Also this
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
501 allows to use the tool for querying data sets (and their accessions) of interest which
ac24fff14f23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
iuc
parents: 10
diff changeset
502 can then be downloaded in a second call using the accessions.
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
503 ]]>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
504 </help>
13
1e188c9610c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9
iuc
parents: 12
diff changeset
505 <expand macro="citations"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
506 </tool>