Mercurial > repos > artbio > fetch_fasta_from_ncbi
diff fetch_fasta_from_NCBI.xml @ 4:c667d0ee39f5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ca3070e85c370b914ffa0562afe12b363e05aea4
| author | artbio |
|---|---|
| date | Wed, 29 Nov 2017 17:38:52 -0500 |
| parents | 8be88084f89c |
| children | 706fe8139955 |
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--- a/fetch_fasta_from_NCBI.xml Wed Nov 08 13:00:26 2017 -0500 +++ b/fetch_fasta_from_NCBI.xml Wed Nov 29 17:38:52 2017 -0500 @@ -1,16 +1,71 @@ -<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.2.1"> +<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.3.0"> <description></description> <command><![CDATA[ - python '$__tool_directory__'/fetch_fasta_from_NCBI.py - -i "$queryString" - -d $dbname - -l '$logfile' - $dry_run - -o '$outfile' + python '$__tool_directory__'/fetch_fasta_from_NCBI.py + -i "$queryString" + -d $dbname + -l '$logfile' + -c + -o '$outfile'; + #if $dry_run == "" + number_UIDs=\$(tail -n 2 $logfile | perl -ne '/Found (\d+) UID/ && print \$1'); + python '$__tool_directory__'/fetch_fasta_from_NCBI.py + -i "$queryString" + -d $dbname + -u + -l '$logfile' + -o 'uid_outfile'; + UID_array=( \$(head uid_outfile) ); + array_len=\${#UID_array[@]}; + counter=0; + number_of_groups=\$((array_len / 200000)); + modulo=\$((array_len % 200000)); + if [ "\$modulo" -gt 0 ];then + number_of_groups=\$((number_of_groups + 1)); + fi; + group_number=1; + echo "----- Number of groups of batches: \$number_of_groups -----" >> $logfile; + for ((i=0; i+200000<array_len;i+=200000)); do + echo "----- Group number: \$group_number -----" >> $logfile; + echo "\${UID_array[@]:\$i:99999}" > uid_list_1.txt; + echo "\${UID_array[@]:\$((i+100000)):99999}" > uid_list_2.txt; + python '$__tool_directory__'/fetch_fasta_from_NCBI.py + -d $dbname + -l '$logfile' + -o 'tmp1_outfile' + --UID_list uid_list_1.txt& + python '$__tool_directory__'/fetch_fasta_from_NCBI.py + -d $dbname + -l 'tmp1_logfile' + -o 'tmp2_outfile' + --UID_list uid_list_2.txt& + wait; + cat tmp1_outfile tmp2_outfile>> $outfile; + rm tmp1_outfile tmp2_outfile; + cat tmp1_logfile >> $logfile; + rm tmp1_logfile; + rm uid_list_1.txt uid_list_2.txt; + group_number=\$((group_number + 1)); + counter=\$(( counter + 200000 )); + done; + echo "----- Group number: \$group_number -----" >> $logfile; + echo "----- Last group -----" >> $logfile; + if [ "\$counter" -lt "\$array_len" ]; then + echo "\${UID_array[@]:\$counter:\$((array_len - counter + 1))}" > uid_list.txt; + python '$__tool_directory__'/fetch_fasta_from_NCBI.py + -d $dbname + -l '$logfile' + -o 'tmp_outfile' + --UID_list uid_list.txt; + rm uid_list.txt; + cat tmp_outfile >> $outfile; + rm tmp_outfile; + fi; + #end if ]]></command> <inputs> - <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple:'Drosophila melanogaster[Organism] AND Gcn5[Title]"> + <param name="queryString" type="text" size="5x80" area="True" value="txid10239[orgn] NOT txid131567[orgn] AND complete[all] NOT partial[title] NOT phage[title]" label="Query to NCBI in entrez format" help="exemple: Drosophila melanogaster[Organism] AND Gcn5[Title]"> <sanitizer> <valid initial="string.printable"> <remove value="""/> @@ -26,7 +81,7 @@ <option value="nuccore">Nucleotide</option> <option value="protein">Protein</option> </param> - <param name="dry_run" type="boolean" label="Dry run to get the number of sequences?" truevalue="--count" falsevalue="" checked="false"/> + <param name="dry_run" type="boolean" label="Get only the number of sequences" truevalue="--count" falsevalue="" checked="false"/> </inputs> <outputs> <data name="outfile" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" > @@ -35,23 +90,29 @@ <data format="txt" name="logfile" label="${tool.name}: log"/> </outputs> <tests> - <test> - <param name="queryString" value="9629650[gi]" /> - <param name="dbname" value="nuccore" /> - <output name="outfilename" ftype="fasta" file="output.fa" /> - </test> - <test> - <param name="queryString" value="CU929326[Accession]" /> - <param name="dbname" value="nuccore" /> - <param name="date_filter" value="1"/> - <param name="dry_run" value="True"/> - <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/> - </test> + <test> + <param name="queryString" value="9629650[gi]" /> + <param name="dbname" value="nuccore" /> + <output name="outfilename" ftype="fasta" file="output.fa" /> + </test> + <test> + <param name="queryString" value="CU929326[Accession]" /> + <param name="dbname" value="nuccore" /> + <param name="date_filter" value="1"/> + <param name="dry_run" value="True"/> + <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/> + </test> + <test> + <param name="queryString" value="Drosophila[Organism] AND 2014[PDAT] AND virus" /> + <output name="outfilename" ftype="fasta" > + <metadata name="sequences" value="13" /> + </output> + </test> </tests> <help> **What it does** -This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database for a given entrez query. +This tool retrieves nucleotide/peptide sequences from the corresponding NCBI database (nuccore or protein) for a given entrez query. The tool is preset with "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]" for metaVisitor use purpose @@ -59,8 +120,12 @@ Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields. +By checking the checkbox you can also run your query without sequence retrieval and get the number of sequences your query will fetch. + Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset) +Retrieval progress is reported in the log dataset. + **Acknowledgments** This Galaxy tool has been adapted from the galaxy tool `get_fasta_from_taxon`_.