Mercurial > repos > iuc > ncbi_eutils_esummary
changeset 9:4dc2757b8ce6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0
| author | iuc |
|---|---|
| date | Fri, 04 Oct 2024 14:36:18 +0000 |
| parents | 7fe990069458 |
| children | |
| files | egquery.py esummary.xml macros.xml |
| diffstat | 3 files changed, 2 insertions(+), 76 deletions(-) [+] |
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--- a/egquery.py Mon Jan 23 10:37:10 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,25 +0,0 @@ -#!/usr/bin/env python - -import argparse - -import eutils - - -if __name__ == '__main__': - parser = argparse.ArgumentParser(description='EGQuery', epilog='') - parser.add_argument('term', help='Query') - - parser.add_argument('--user_email', help="User email") - parser.add_argument('--admin_email', help="Admin email") - - parser.add_argument('--version', action='version', version=eutils.Client.getVersion(), help='Version (reports Biopython version)') - - args = parser.parse_args() - - c = eutils.Client(user_email=args.user_email, admin_email=args.admin_email) - - payload = { - 'term': args.term, - } - results = c.gquery(**payload) - print(results)
--- a/esummary.xml Mon Jan 23 10:37:10 2023 +0000 +++ b/esummary.xml Fri Oct 04 14:36:18 2024 +0000 @@ -1,4 +1,3 @@ -<?xml version="1.0"?> <tool id="ncbi_eutils_esummary" name="NCBI ESummary" version="@WRAPPER_VERSION@" profile="@PROFILE@"> <description>fetch summary of history/ids</description> <macros> @@ -59,7 +58,7 @@ </collection> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="qss" value="id_list"/> <param name="id_list" value="10239"/> <param name="db_select" value="taxonomy"/>
--- a/macros.xml Mon Jan 23 10:37:10 2023 +0000 +++ b/macros.xml Fri Oct 04 14:36:18 2024 +0000 @@ -2,7 +2,7 @@ <macros> <token name="@PROFILE@">18.01</token> <token name="@TOOL_VERSION@">1.70</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy@VERSION_SUFFIX@</token> <token name="@EMAIL_ARGUMENTS@"> --user_email "$__user_email__" @@ -4467,54 +4467,6 @@ </when> </conditional> </when> - <when value="annotinfo"> - <conditional name="db_to"> - <param name="db_select_to" type="select" label="To NCBI Database"> - <option value="none">Not applicable</option> - </param> - <when value="none"> - <param name="linkname" type="select" label="Link Name"> - <option value="none">Not applicable</option> - </param> - </when> - </conditional> - </when> - <when value="gapplus"> - <conditional name="db_to"> - <param name="db_select_to" type="select" label="To NCBI Database"> - <option value="none">Not applicable</option> - </param> - <when value="none"> - <param name="linkname" type="select" label="Link Name"> - <option value="none">Not applicable</option> - </param> - </when> - </conditional> - </when> - <when value="ncbisearch"> - <conditional name="db_to"> - <param name="db_select_to" type="select" label="To NCBI Database"> - <option value="none">Not applicable</option> - </param> - <when value="none"> - <param name="linkname" type="select" label="Link Name"> - <option value="none">Not applicable</option> - </param> - </when> - </conditional> - </when> - <when value="grasp"> - <conditional name="db_to"> - <param name="db_select_to" type="select" label="To NCBI Database"> - <option value="none">Not applicable</option> - </param> - <when value="none"> - <param name="linkname" type="select" label="Link Name"> - <option value="none">Not applicable</option> - </param> - </when> - </conditional> - </when> </conditional> </xml> <token name="@LINK_TOKEN@">