Mercurial > repos > iuc > ncbi_datasets
annotate datasets_genome.xml @ 6:5a2656cc84cb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
| author | iuc |
|---|---|
| date | Mon, 06 Jun 2022 13:41:05 +0000 |
| parents | 6c829a430475 |
| children | 0622d99c2619 |
| rev | line source |
|---|---|
|
6
5a2656cc84cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents:
5
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1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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2 <description>download genome sequence, annotation and metadata</description> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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3 <macros> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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4 <import>macros.xml</import> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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5 </macros> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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6 <expand macro="requirements"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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7 <command><![CDATA[ |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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8 @SETUP_CERTIFICATES@ |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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9 datasets download genome $query.subcommand.download_by |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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10 #if $query.subcommand.download_by == 'accession': |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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11 #if $query.subcommand.text_or_file.text_or_file == 'text': |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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12 #echo " ".join(f"'{x}'" for x in $query.subcommand.text_or_file.accession.split(' ') if x) |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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13 #else |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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14 --inputfile '$query.subcommand.text_or_file.inputfile' |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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15 #end if |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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16 #else: |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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17 '$query.subcommand.taxon' |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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18 #end if |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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19 $filters.reference |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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20 $filters.annotated |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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21 #if $filters.assembly_level: |
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5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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22 --assembly-level $filters.assembly_level |
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0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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23 #end if |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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24 #if $filters.assembly_source: |
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5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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25 --assembly-source $filters.assembly_source |
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0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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26 #end if |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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27 #if $filters.chromosomes: |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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28 --chromosomes '$filters.chromosomes' |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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29 #end if |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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30 @EXCLUDES_GENOME@ |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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31 @INCLUDES_GENOME@ |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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32 @RELEASED_BEFORE@ |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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33 @RELEASED_SINCE@ |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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34 #for search_term in $filters.search: |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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35 --search '$filters.search_term' |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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36 #end for |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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37 #if $uncompressed |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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38 && unzip ncbi_dataset.zip |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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39 #else |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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40 && unzip -l ncbi_dataset.zip > ncbi_dataset.txt |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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41 #end if |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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42 ]]></command> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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43 <inputs> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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44 <section name="query" title="Query" expanded="true"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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45 <conditional name="subcommand"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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46 <param name="download_by" type="select" label="Choose how to find genomes to download"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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47 <option value="accession">Download by NCBI assembly or BioProject accession</option> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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48 <option value="taxon">Download by taxon</option> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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49 </param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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50 <when value="accession"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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51 <expand macro="text_or_file"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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52 </when> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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53 <when value="taxon"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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54 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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55 </when> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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56 </conditional> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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57 </section> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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58 <section name="filters" title="Filters and Limit"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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59 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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60 <expand macro="annotation"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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61 <expand macro="assembly_level"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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62 <expand macro="assembly_source"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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63 <expand macro="chromosomes"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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64 <expand macro="released_options"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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65 <expand macro="released_options" before_or_after="since"></expand> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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66 |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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67 <repeat name="search" title="Add search terms"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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68 <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"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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69 </repeat> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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70 </section> |
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5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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71 <section name="file_choices" title="File Choices" expanded="true"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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72 <expand macro="excludes_genome"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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73 <expand macro="includes_genome"></expand> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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74 </section> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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75 <param name="uncompressed" type="boolean" label="Uncompress the dataset archive" checked="true"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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76 </inputs> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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77 <outputs> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
78 <data name="compressed_archive" format="zip" label="Compressed Archive" from_work_dir="ncbi_dataset.zip"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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79 <filter>not uncompressed</filter> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
80 </data> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff
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|
81 <data name="archive_contents" format="txt" label="Archive Contents" from_work_dir="ncbi_dataset.txt"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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82 <filter>not uncompressed</filter> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
83 </data> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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84 <data name="genome_data_report" format="json" label="NCBI Genome Datasets: Data Report" from_work_dir="ncbi_dataset/data/assembly_data_report.jsonl"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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85 <filter>uncompressed</filter> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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86 </data> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
87 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
88 <discover_datasets pattern="(?P<identifier_0>.*?)\/sequence_report.jsonl" ext="json" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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89 <filter>uncompressed</filter> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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90 </collection> |
|
6
5a2656cc84cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents:
5
diff
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91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list"> |
|
5a2656cc84cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents:
5
diff
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|
92 <discover_datasets pattern="(?P<identifier_0>.*?)\/(?P<identifier_1>.*?)\.(?<!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
93 <filter>uncompressed and not file_choices['exclude_seq']</filter> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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94 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff
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|
95 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
96 <discover_datasets pattern="(?P<identifier_0>.*?)\/cds_from_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
97 <filter>uncompressed and not file_choices['exclude_genomic_cds']</filter> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
98 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff
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|
99 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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100 <discover_datasets pattern="(?P<identifier_0>.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
101 <filter>uncompressed and not file_choices['exclude_gff3']</filter> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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102 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff
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|
103 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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104 <discover_datasets pattern="(?P<identifier_0>.*?)\/rna\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
105 <filter>uncompressed and not file_choices['exclude_rna']</filter> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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106 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff
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|
107 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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108 <discover_datasets pattern="(?P<identifier_0>.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
109 <filter>uncompressed and not file_choices['exclude_protein']</filter> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
110 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff
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|
111 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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112 <discover_datasets pattern="(?P<identifier_0>.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
113 <filter>uncompressed and file_choices['include_gbff']</filter> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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114 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
115 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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116 <discover_datasets pattern="(?P<identifier_0>.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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117 <filter>uncompressed and file_choices['include_gtf']</filter> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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118 </collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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119 </outputs> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
120 <tests> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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121 <test expect_num_outputs="2"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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|
122 <conditional name="query|subcommand"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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123 <param name="download_by" value="taxon"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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124 <param name="text_or_file" value="text"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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125 <param name="taxon" value="human"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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126 </conditional> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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127 <param name="chromosomes" value="21"></param> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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|
128 <param name="exclude_protein" value="true"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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129 <param name="exclude_rna" value="true"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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130 <param name="exclude_seq" value="true"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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131 <param name="exclude_genomic_cds" value="true"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
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132 <param name="exclude_gff3" value="true"/> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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parents:
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133 <param name="uncompressed" value="false"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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134 <param name="released_before" value="01/01/2018"></param> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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135 <output name="archive_contents"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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136 <assert_contents> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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137 <has_text text="ncbi_dataset/data/dataset_catalog.json"/> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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138 </assert_contents> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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139 </output> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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140 </test> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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|
141 <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
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|
142 <conditional name="query|subcommand"> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
143 <param name="download_by" value="taxon"></param> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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|
144 <param name="text_or_file" value="text"></param> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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|
145 <param name="taxon" value="human"></param> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
diff
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|
146 </conditional> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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|
147 <param name="chromosomes" value="21"></param> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
0
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|
148 <param name="uncompressed" value="false"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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149 <param name="exclude_protein" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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150 <param name="exclude_rna" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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151 <param name="exclude_seq" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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152 <param name="exclude_genomic_cds" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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153 <param name="exclude_gff3" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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154 <param name="assembly_level" value="chromosome"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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155 <param name="released_before" value="01/01/2018"></param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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156 <output name="archive_contents"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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157 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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158 <has_text text="ncbi_dataset/data/dataset_catalog.json"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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159 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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160 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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161 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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162 <test expect_num_outputs="4"> |
|
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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163 <conditional name="query|subcommand"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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164 <param name="download_by" value="accession"></param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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165 <conditional name="text_or_file"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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166 <param name="text_or_file" value="text"></param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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167 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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168 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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169 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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170 <param name="uncompressed" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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171 <param name="released_before" value="01/01/2007"></param> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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172 <param name="exclude_protein" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
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173 <param name="exclude_rna" value="true"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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174 <param name="exclude_seq" value="true"/> |
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6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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175 <param name="exclude_gff3" value="true"/> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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176 <param name="include_gtf" value="true"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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177 <output name="genome_data_report"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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178 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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179 <has_text text="GCF_000013305.1"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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180 </assert_contents> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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181 </output> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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182 <output_collection name="genomic_gtf" type="list"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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183 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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184 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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185 </output_collection> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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186 <output_collection name="genomic_cds" type="list"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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187 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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188 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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189 </output_collection> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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190 </test> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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191 <test expect_num_outputs="4"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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192 <conditional name="query|subcommand"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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193 <param name="download_by" value="accession"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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194 <conditional name="text_or_file"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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195 <param name="text_or_file" value="file"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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196 <param name="inputfile" value="accessions.txt"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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197 </conditional> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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198 </conditional> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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199 <param name="include_gbff" value="true"/> |
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5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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200 <param name="exclude_protein" value="true"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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201 <param name="exclude_rna" value="true"/> |
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6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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202 <param name="exclude_seq" value="true"/> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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203 <param name="exclude_genomic_cds" value="true"/> |
|
0
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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204 <param name="uncompressed" value="true"/> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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205 <param name="released_before" value="01/02/2007"></param> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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206 <output name="genome_data_report"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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207 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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208 <has_text text="SAMN02604181"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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209 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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210 </output> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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211 <output_collection name="genomic_gff" type="list"> |
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1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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212 <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"
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213 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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214 </output_collection> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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215 <output_collection name="genomic_gbff" type="list"> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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216 <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"
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217 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/> |
|
1a7773882d2c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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218 </output_collection> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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219 </test> |
|
5
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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220 <test expect_num_outputs="2"> |
|
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
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221 <conditional name="query|subcommand"> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
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222 <param name="download_by" value="accession"></param> |
|
6c829a430475
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents:
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223 <conditional name="text_or_file"> |
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224 <param name="text_or_file" value="text"></param> |
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225 <param name="accession" value="GCF_000001405.40"></param> |
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226 </conditional> |
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227 </conditional> |
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228 <param name="exclude_protein" value="true"/> |
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229 <param name="exclude_rna" value="true"/> |
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230 <param name="exclude_seq" value="true"/> |
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231 <param name="exclude_genomic_cds" value="true"/> |
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232 <param name="exclude_gff3" value="true"/> |
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233 <param name="uncompressed" value="true"/> |
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234 <param name="released_before" value="01/02/2007"></param> |
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235 <output_collection name="sequence_report"> |
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236 <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/> |
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237 </output_collection> |
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238 </test> |
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239 <test expect_num_outputs="3"> |
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240 <conditional name="query|subcommand"> |
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241 <param name="download_by" value="accession"></param> |
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242 <conditional name="text_or_file"> |
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243 <param name="text_or_file" value="text"></param> |
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244 <param name="accession" value="GCF_000146045.2"></param> |
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245 </conditional> |
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246 </conditional> |
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247 <param name="exclude_protein" value="true"/> |
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248 <param name="exclude_rna" value="true"/> |
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249 <param name="exclude_seq" value="false"/> |
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250 <param name="exclude_genomic_cds" value="true"/> |
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251 <param name="exclude_gff3" value="true"/> |
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252 <param name="uncompressed" value="true"/> |
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253 <output_collection name="genome_fasta" type="list:list" count="1"> |
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254 <element name="GCF_000146045.2"> |
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255 <element name="chrI"> |
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256 <assert_contents> |
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257 <has_text text=">NC_001133.9"/> |
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258 </assert_contents> |
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259 </element> |
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260 </element> |
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261 </output_collection> |
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262 </test> |
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263 </tests> |
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264 <help> |
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265 <![CDATA[ |
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266 **Download Genome Datasets from NCBI** |
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267 |
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268 Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report. |
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269 Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file. |
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270 |
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271 Tthe default genome dataset includes the following files (if available): |
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272 * data_report.jsonl (genome assembly and annotation metadata, not always available) |
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273 * genomic.fna (genomic sequences) |
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274 * rna.fna (transcript sequences) |
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275 * protein.faa (protein sequences) |
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276 * genomic.gff (genome annotation in gff3 format) |
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277 * dataset_catalog.json (a list of files and file types included in the dataset) |
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278 ]]> |
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279 </help> |
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280 |
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281 </tool> |