comparison 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

2:befdb392fece

<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>

  <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]">
      <sanitizer>
        <valid initial="string.printable">

This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.

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
.. _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

  </help>

3:a9d8f69d59fb

<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.4">
  <description></description>
  <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]">
      <sanitizer>
        <valid initial="string.printable">

This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.

It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.

.. _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

  </help>