Mercurial > repos > drosofff > fetch_fasta_from_ncbi
comparison retrieve_fasta_from_NCBI.xml @ 1:79cb7620843d draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit e0a1114b735bf1af257456174f64e5ef8d205754-dirty
| author | drosofff |
|---|---|
| date | Wed, 28 Oct 2015 11:25:13 -0400 |
| parents | 0bdc5a73c8d1 |
| children | befdb392fece |
comparison
equal
deleted
inserted
replaced
| 0:0bdc5a73c8d1 | 1:79cb7620843d |
|---|---|
| 1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.2"> | 1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="0.9.3"> |
| 2 <description></description> | 2 <description></description> |
| 3 <command interpreter="python">retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile </command> | 3 <command interpreter="python">retrieve_fasta_from_NCBI.py -i "$queryString" -d $dbname -o $outfilename -l $logfile </command> |
| 4 | 4 |
| 5 <inputs> | 5 <inputs> |
| 6 <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]"> | 6 <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]"> |
| 16 </sanitizer> | 16 </sanitizer> |
| 17 </param> | 17 </param> |
| 18 <param name="dbname" type="select" label="NCBI database"> | 18 <param name="dbname" type="select" label="NCBI database"> |
| 19 <option value="nuccore">Nucleotide</option> | 19 <option value="nuccore">Nucleotide</option> |
| 20 <option value="protein">Protein</option> | 20 <option value="protein">Protein</option> |
| 21 <!-- <option value="pubmed">Pubmed (experimental)</option> --> | |
| 22 </param> | 21 </param> |
| 23 </inputs> | 22 </inputs> |
| 24 <outputs> | 23 <outputs> |
| 25 <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: queryString${queryString.value}.${dbname.value_label}.fasta" /> | 24 <data name="outfilename" format="fasta" label="${tool.name} on ${on_string}: queryString${queryString.value}.${dbname.value_label}.fasta" /> |
| 26 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/> | 25 <data format="txt" name="logfile" label="${tool.name} on ${on_string}: log"/> |