Mercurial > repos > iuc > ncbi_eutils_ecitmatch
changeset 2:1dff3adb0a97 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
| author | iuc |
|---|---|
| date | Wed, 11 Mar 2020 04:03:55 -0400 |
| parents | 732a52c18758 |
| children | b00212deaea7 |
| files | __pycache__/eutils.cpython-35.pyc ecitmatch.xml eutils.py macros.xml test-data/pubmed.metadata.xml |
| diffstat | 5 files changed, 7 insertions(+), 8 deletions(-) [+] |
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--- a/ecitmatch.xml Tue Oct 30 19:11:26 2018 -0400 +++ b/ecitmatch.xml Wed Mar 11 04:03:55 2020 -0400 @@ -1,12 +1,13 @@ <?xml version="1.0"?> -<tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@"> +<tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@" profile="@PROFILE@"> <description>search NCBI for citations in PubMed</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>python ecitmatch.py --version</version_command> - <command detect_errors="aggressive" interpreter="python"><![CDATA[ecitmatch.py + <command detect_errors="aggressive"><![CDATA[ +python '$__tool_directory__/ecitmatch.py' #if str($input.method) == "file": --file $input.citation_file
--- a/eutils.py Tue Oct 30 19:11:26 2018 -0400 +++ b/eutils.py Wed Mar 11 04:03:55 2020 -0400 @@ -1,8 +1,8 @@ import json import os +from io import StringIO from Bio import Entrez -from six import StringIO Entrez.tool = "GalaxyEutils_1_0" BATCH_SIZE = 200
--- a/macros.xml Tue Oct 30 19:11:26 2018 -0400 +++ b/macros.xml Wed Mar 11 04:03:55 2020 -0400 @@ -1,6 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.2</token> + <token name="@PROFILE@">18.01</token> + <token name="@WRAPPER_VERSION@">1.3</token> <token name="@EMAIL_ARGUMENTS@"> --user_email "$__user_email__" #set admin_emails = ';'.join(str($__admin_users__).split(',')) @@ -835,8 +836,7 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="1.68">biopython</requirement> - <requirement type="package" version="1.10">six</requirement> + <requirement type="package" version="1.70">biopython</requirement> </requirements> </xml> <xml name="linkname">
--- a/test-data/pubmed.metadata.xml Tue Oct 30 19:11:26 2018 -0400 +++ b/test-data/pubmed.metadata.xml Wed Mar 11 04:03:55 2020 -0400 @@ -1,5 +1,3 @@ -<?xml version="1.0" encoding="UTF-8" ?> -<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD einfo 20130322//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20130322/einfo.dtd"> <eInfoResult> <DbInfo> <DbName>pubmed</DbName>