Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

comparison data_manager/ncbi_taxonomy_fetcher.xml @ 6:6dd9e00dea95 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 3d78021971b83d585c432830cee0488ada7bd257"
author iuc
date Fri, 19 Mar 2021 21:43:42 +0000
parents 9de2fb1ce1fb
children 34a5799a65fa
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5:9de2fb1ce1fb 6:6dd9e00dea95
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2"> 2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.3">
3 <description>taxonomy downloader</description> 3 <description>taxonomy downloader</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.7">python</requirement> 5 <requirement type="package" version="3.7">python</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
11 --url '${taxonomy_url}' 11 --url '${taxonomy_url}'
12 #end if 12 #end if
13 #if $database_name: 13 #if $database_name:
14 --name '${database_name}' 14 --name '${database_name}'
15 #end if 15 #end if
16 $name_maps
17 $partial_data
16 ]]> 18 ]]>
17 </command> 19 </command>
18 <inputs> 20 <inputs>
19 <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" /> 21 <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
20 <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" /> 22 <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
23 <param name="name_maps" type="boolean" truevalue="--name-maps" falsevalue="" label="Also download accession2taxid data" checked="false" />
24 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
21 </inputs> 25 </inputs>
22 <outputs> 26 <outputs>
23 <data name="out_file" format="data_manager_json" /> 27 <data name="out_file" format="data_manager_json" />
24 </outputs> 28 </outputs>
25 <tests> 29 <tests>
26 <test> 30 <test>
27 <param name="database_name" value="tax_name"/> 31 <param name="database_name" value="tax_name"/>
28 <param name="database_id" value="tax_id"/> 32 <param name="database_id" value="tax_id"/>
29 <output name="out_file" value="taxonomy.json"/> 33 <output name="out_file" value="taxonomy.json"/>
30 </test> 34 </test>
35 <test>
36 <param name="database_name" value="tax_name"/>
37 <param name="database_id" value="tax_id"/>
38 <param name="name_maps" value="true"/>
39 <param name="partial_data" value="--partial"/>
40 <output name="out_file" value="taxonomy_with_accession2taxid.json"/>
41 </test>
31 </tests> 42 </tests>
32 <help> 43 <help>
33 Download a taxonomy dump from a provided URL. 44 Download a taxonomy dump from a provided URL.
34 The default URL is the latest dump from NCBI taxonomy. 45 The default URL is the latest dump from NCBI taxonomy.
46 The accession2taxid data comes from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ and can be used by the Diamond data_manager (uses ~20Gb as of 2021).
35 </help> 47 </help>
36 </tool> 48 </tool>