--- /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>