Mercurial > repos > crs4 > prokka
diff prokka.xml @ 0:95505a9fa26f draft
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author | crs4 |
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date | Tue, 10 Sep 2013 13:11:26 -0400 |
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children | 4b6f16a79fe4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prokka.xml Tue Sep 10 13:11:26 2013 -0400 @@ -0,0 +1,112 @@ +<tool id="prokka" name="Prokka" version="1.0.0"> + <description>Prokaryotic Annotation</description> + <requirements> + <requirement type="package" version="2.2.26+">blast+</requirement> + <requirement type="package" version="3.1b1">hmmer</requirement> + <requirement type="package" version="1.2.36">aragorn</requirement> + <requirement type="package" version="1.1rc4">infernal</requirement> + <requirement type="package" version="1.7">prokka</requirement> + </requirements> + <version_command>prokka --version</version_command> + <command interpreter="python"> + prokka.py + \${PROKKA_SITE_OPTIONS:---cpus 8} + ## Reads in FASTA format + --fasta=$fasta_file + ## Additional inputs + --kingdom $kingdom_type.kingdom + #if str($mincontig) + --mincontig $mincontig + #end if + #if $rfam + --rfam + #end if + #if $centre + --centre "$centre" + #end if + ## Output files + --gff=$out_gff + --gbk=$out_gbk + --fna=$out_fna + --faa=$out_faa + --ffn=$out_ffn + --sqn=$out_sqn + --fsa=$out_fsa + --tbl=$out_tbl + --err=$out_err + --log=$out_log + </command> + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Contigs" help="FASTA format" /> + <conditional name="kingdom_type"> + <param name="kingdom" type="select" label="Kingdom (--kingdom)"> + <option value="Archaea">Archaea</option> + <option value="Bacteria" selected="true">Bacteria</option> + <option value="Viruses">Viruses</option> + </param> + <when value="Archaea" /> + <when value="Bacteria" /> + <when value="Viruses" /> + </conditional> + <param name="mincontig" type="integer" value="200" optional="true" label="Minimun contig size - NCBI needs 200 (--mincontig)" /> + <param name="centre" type="text" value="CRS4" label="Sequencing centre ID (--centre)" /> + <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal-Rfam - SLOW (--rfam)" /> + </inputs> + <outputs> + <data format="gff" name="out_gff" label="${tool.name} on ${on_string}: gff"/> + <data format="txt" name="out_gbk" label="${tool.name} on ${on_string}: gbk"/> + <data format="fasta" name="out_fna" label="${tool.name} on ${on_string}: fna"/> + <data format="fasta" name="out_faa" label="${tool.name} on ${on_string}: faa"/> + <data format="fasta" name="out_ffn" label="${tool.name} on ${on_string}: ffn"/> + <data format="asn1" name="out_sqn" label="${tool.name} on ${on_string}: sqn"/> + <data format="fasta" name="out_fsa" label="${tool.name} on ${on_string}: fsa"/> + <data format="txt" name="out_tbl" label="${tool.name} on ${on_string}: tbl"/> + <data format="txt" name="out_err" label="${tool.name} on ${on_string}: err"/> + <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/> + </outputs> + + <help> +**What it does** + +Prokka_ is a software tool to annotate bacterial, archaeal and viral genomes very rapidly, and produce output files that require only minor tweaking to submit to Genbank/ENA/DDBJ. + +.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml + +**Output files** + +Prokka creates several output files:: + + gff This is the master annotation in GFF3 format, containing both sequences and annotations. + It can be viewed directly in Artemis or IGV + gbk This is a standard Genbank file derived from the master .gff + If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, + with one record for each sequence + fna Nucleotide FASTA file of the input contig sequences + faa Protein FASTA file of the translated CDS sequences + ffn Nucleotide FASTA file of all the annotated sequences, not just CDS + sqn An ASN1 format "Sequin" file for submission to Genbank. + It needs to be edited to set the correct taxonomy, authors, related publication etc. + fsa Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. + It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines + tbl Feature Table file, used by "tbl2asn" to create the .sqn file. + err Unacceptable annotations - the NCBI discrepancy report. + log Contains all the output that Prokka produced during its run. + This is a record of what settings you used. + +**License and citation** + +This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +If you use this tool in Galaxy, please cite |Cuccuru2013|_. + +.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* +.. _Cuccuru2013: http://orione.crs4.it/ + +This tool uses `Prokka`_, which is licensed separately. Please cite Seemann T. Prokka: Prokaryotic Genome Annotation System (in preparation). + +.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml + </help> +</tool>