Mercurial > repos > iuc > ncbi_eutils_efetch

changeset 2:0977ec0f3ba8 draft

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"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 04:03:36 -0400
parents 0fc65a60436f
children c09fcbe4b16a
files __pycache__/eutils.cpython-35.pyc efetch.xml eutils.py macros.xml test-data/pubmed.metadata.xml
diffstat 5 files changed, 7 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
Binary file __pycache__/eutils.cpython-35.pyc has changed
--- a/efetch.xml	Tue Oct 30 19:08:30 2018 -0400
+++ b/efetch.xml	Wed Mar 11 04:03:36 2020 -0400
@@ -1,12 +1,13 @@
 <?xml version="1.0"?>
-<tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@">
+<tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
   <description>fetch records from NCBI</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
   <version_command>python efetch.py --version</version_command>
-  <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
+  <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/efetch.py'
 $db.db_select
 
 @LIST_OR_HIST@
--- a/eutils.py	Tue Oct 30 19:08:30 2018 -0400
+++ b/eutils.py	Wed Mar 11 04:03:36 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 19:08:30 2018 -0400
+++ b/macros.xml	Wed Mar 11 04:03:36 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 19:08:30 2018 -0400
+++ b/test-data/pubmed.metadata.xml	Wed Mar 11 04:03:36 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>