# HG changeset patch
# User drosofff
# Date 1478708851 18000
# Node ID a9d8f69d59fbb9ba32b0885984612341c11c4703
# Parent  befdb392fecebaf3a1c2d47f518e17667f87b35d
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07

diff -r befdb392fece -r a9d8f69d59fb retrieve_fasta_from_NCBI.py
--- a/retrieve_fasta_from_NCBI.py	Tue Jan 05 10:06:42 2016 -0500
+++ b/retrieve_fasta_from_NCBI.py	Wed Nov 09 11:27:31 2016 -0500
@@ -32,11 +32,13 @@
 import urllib2
 import httplib
 import re
+
+
 class Eutils:
 
     def __init__(self, options, logger):
         self.logger = logger
-        self.base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
+        self.base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
         self.query_string = options.query_string
         self.dbname = options.dbname
         if options.outname:
diff -r befdb392fece -r a9d8f69d59fb retrieve_fasta_from_NCBI.xml
--- a/retrieve_fasta_from_NCBI.xml	Tue Jan 05 10:06:42 2016 -0500
+++ b/retrieve_fasta_from_NCBI.xml	Wed Nov 09 11:27:31 2016 -0500
@@ -1,6 +1,12 @@
 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.4">
   <description></description>
-  <command interpreter="python">retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile </command>
+  <command><![CDATA[
+      python '$__tool_directory__'/retrieve_fasta_from_NCBI.py
+      -i "$queryString"
+      -d $dbname
+      -o '$outfilename'
+      -l '$logfile'
+  ]]></command>
 
   <inputs>
     <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]">
@@ -51,7 +57,7 @@
 
 It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.
 
-.. _Entrez help: http://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
+.. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
 .. _get_fasta_from_taxon: https://toolshed.g2.bx.psu.edu/view/crs4/get_fasta_from_taxon
 .. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en
 .. _MIT license: http://opensource.org/licenses/MIT
diff -r befdb392fece -r a9d8f69d59fb test-data/output.fa
--- a/test-data/output.fa	Tue Jan 05 10:06:42 2016 -0500
+++ b/test-data/output.fa	Wed Nov 09 11:27:31 2016 -0500
@@ -1,4 +1,4 @@
->gi|9629650|ref|NC_001834.1|_Drosophila_C_virus,_complete_genome
+>NC_001834.1_Drosophila_C_virus,_complete_genome
 TTTATATCGTGTGTACATATAAATATGTACACACGGCTTTTAGGTAGAATATTGTTTTCAATGTTGATTT
 TAAAGGTAACTTTGGTTATTATGCTTTACGGTTTTCATTGTTGATGGTATTTGTGGCCTGCGGTCCCTAA
 TTGTTGAATTATTTATTCTGATACGTTGTTTTCATTGTTGATGGTAAGGATTCTTATTTTGAAGTGGTTT