diff retrieve_fasta_from_NCBI.xml @ 3:a9d8f69d59fb draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b6de14061c479f0418cd89e26d6f5ac26e565a07

--- 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