comparison retrieve_fasta_from_NCBI.xml @ 2:befdb392fece draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit fae2061eadac000cdb408d0db76226620c8860a6

1:79cb7620843d

<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.3">
  <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]">

      <option value="nuccore">Nucleotide</option>
      <option value="protein">Protein</option>
    </param>
  </inputs>
  <outputs>
    <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: queryString${queryString.value}.${dbname.value_label}.fasta" />
    <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/>
  </outputs>
  <tests>
    <test>
        <param name="queryString" value="9629650[gi]" />
        <param name="dbname" value="nuccore" />

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]">

      <option value="nuccore">Nucleotide</option>
      <option value="protein">Protein</option>
    </param>
  </inputs>
  <outputs>
    <data name="outfilename" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" />
    <data format="txt" name="logfile" label="${tool.name}: log"/>
  </outputs>
  <tests>
    <test>
        <param name="queryString" value="9629650[gi]" />
        <param name="dbname" value="nuccore" />