Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

diff 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
line wrap: on
line diff
--- a/data_manager/ncbi_taxonomy_fetcher.xml	Sun Nov 22 12:48:48 2020 +0000
+++ b/data_manager/ncbi_taxonomy_fetcher.xml	Fri Mar 19 21:43:42 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2">
+<tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.3">
     <description>taxonomy downloader</description>
     <requirements>
         <requirement type="package" version="3.7">python</requirement>
@@ -13,11 +13,15 @@
         #if $database_name:
             --name '${database_name}'
         #end if
+        $name_maps
+        $partial_data
     ]]>
     </command>
     <inputs>
         <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" />
         <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
+        <param name="name_maps" type="boolean" truevalue="--name-maps" falsevalue="" label="Also download accession2taxid data" checked="false" />
+        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />
@@ -28,9 +32,17 @@
             <param name="database_id" value="tax_id"/>
             <output name="out_file" value="taxonomy.json"/>
         </test>
+        <test>
+            <param name="database_name" value="tax_name"/>
+            <param name="database_id" value="tax_id"/>
+            <param name="name_maps" value="true"/>
+            <param name="partial_data" value="--partial"/>
+            <output name="out_file" value="taxonomy_with_accession2taxid.json"/>
+        </test>
     </tests>
     <help>
         Download a taxonomy dump from a provided URL.
         The default URL is the latest dump from NCBI taxonomy.
+        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).
     </help>
 </tool>