--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prokka.xml	Tue Jul 09 12:31:34 2019 -0400
@@ -0,0 +1,230 @@
+<tool id="prokka" name="Prokka" version="1.13">
+    <description>Prokaryotic genome annotation</description>
+    <requirements>
+        <requirement type="package" version="1.13">prokka</requirement>
+    </requirements>
+
+    <version_command>prokka --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+prokka
+--cpus \${GALAXY_SLOTS:-8}
+--quiet ## to avoid non-error messages written to stderr
+--outdir outdir --prefix prokka ## used in outputs section
+#if $locustag
+    --locustag '$locustag'
+#end if
+#if str($increment)
+    --increment $increment
+#end if
+--gffver $gffver
+#if $compliant.compliant_select == "no"
+    #if $compliant.addgenes
+        --addgenes
+    #end if
+    #if str($compliant.mincontig)
+        --mincontig $compliant.mincontig
+    #end if
+#else
+    --compliant
+#end if
+#if $centre
+    --centre '$centre'
+#end if
+#if $genus
+    --genus '$genus'
+#end if
+#if $species
+    --species '$species'
+#end if
+#if $strain
+    --strain '$strain'
+#end if
+#if $plasmid
+    --plasmid '$plasmid'
+#end if
+--kingdom $kingdom.kingdom_select
+#if str($kingdom.gcode)
+    --gcode $kingdom.gcode
+#end if
+#if $usegenus
+    --usegenus
+#end if
+#if $proteins
+    --proteins '$proteins'
+#end if
+#if $metagenome
+    --metagenome
+#end if
+#if $fast
+    --fast
+#end if
+#if str($evalue)
+    --evalue $evalue
+#end if
+#if $rfam
+    --rfam
+#end if
+#if $norrna
+    --norrna
+#end if
+#if $notrna
+    --notrna
+#end if
+$input
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
+        <param name="locustag" type="text" value="" label="Locus tag prefix (--locustag)" />
+        <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" />
+        <param name="gffver" type="select" label="GFF version (--gffver)">
+            <option value="3">3</option>
+            <option value="2">2</option>
+            <option value="1">1</option>
+        </param>
+        <conditional name="compliant">
+            <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+                <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
+                <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
+            </when>
+            <when value="yes" />
+        </conditional>
+        <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
+        <param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
+        <param name="species" type="text" value="" label="Species name (--species)" />
+        <param name="strain" type="text" value="" label="Strain name (--strain)" />
+        <param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
+        <conditional name="kingdom">
+            <param name="kingdom_select" 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">
+                <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+            <when value="Bacteria">
+                <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+                <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)">
+                    <option selected="true" value="none">N/A</option>
+                    <option value="pos">positive</option>
+                    <option value="neg">negative</option>
+                </param> SignalP is not FOSS -->
+            </when>
+            <when value="Viruses">
+                <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
+            </when>
+        </conditional>
+        <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
+        <param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
+        <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
+        <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
+        <param name="evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" />
+        <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" />
+        <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" />
+        <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" />
+
+        <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
+            <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option>
+            <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence (.gbk)</option>
+            <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option>
+            <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option>
+            <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option>
+            <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc. (.sqn)</option>
+            <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option>
+            <option value="tbl" selected="True">Feature Table file (.tbl)</option>
+            <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option>
+            <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option>
+            <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
+            <filter>outputs and 'gff' in outputs</filter>
+        </data>
+        <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk">
+            <filter>outputs and 'gbk' in outputs</filter>
+        </data>
+        <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna">
+            <filter>outputs and 'fna' in outputs</filter>
+        </data>
+        <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa">
+            <filter>outputs and 'faa' in outputs</filter>
+        </data>
+        <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn">
+             <filter>outputs and 'ffn' in outputs</filter>
+        </data>
+        <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn">
+             <filter>outputs and 'sqn' in outputs</filter>
+        </data>
+        <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa">
+             <filter>outputs and 'fsa' in outputs</filter>
+        </data>
+        <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
+             <filter>outputs and 'tbl' in outputs</filter>
+        </data>
+        <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv">
+             <filter>outputs and 'tsv' in outputs</filter>
+        </data>
+        <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err">
+             <filter>outputs and 'err' in outputs</filter>
+        </data>
+        <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt">
+             <filter>outputs and 'txt' in outputs</filter>
+        </data>
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="fasta" value="phiX174.fasta" />
+            <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" />
+            <output name="out_gff" file="out.gff" />
+            <output name="out_gbk" file="out.gbk" lines_diff="14" />
+            <output name="out_fna" file="out.fna" />
+            <output name="out_faa" file="out.faa" />
+            <output name="out_ffn" file="out.ffn" />
+            <output name="out_sqn" file="out.sqn" lines_diff="84" />
+            <output name="out_fsa" file="out.fsa" />
+            <output name="out_tbl" file="out.tbl" />
+            <output name="out_tsv" file="out.tsv" />
+            <output name="out_err" file="out.err" />
+            <output name="out_txt" file="out.txt" />
+            <output name="out_log">
+                <assert_contents>
+                    <has_text text="Type 'prokka --citation' for more details." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ.
+
+.. _Prokka: http://github.com/tseemann/prokka
+
+**Output files**
+
+Prokka creates several output files, which are described in the **Additional outputs** section above.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _Earlham Institute: http://earlham.ac.uk/
+.. _MIT license: https://opensource.org/licenses/MIT
+
+You can use this tool only if you agree to the license terms of: `Prokka`_.
+
+.. _Prokka: http://github.com/tseemann/prokka
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+        <citation type="doi">10.1093/bioinformatics/btu153</citation>
+    </citations>
+</tool>