Mercurial > repos > crs4 > prokka
diff prokka.xml @ 8:392255fa7ab9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
| author | iuc |
|---|---|
| date | Fri, 28 Oct 2016 13:03:19 -0400 |
| parents | f5e44aad6498 |
| children | fd4b2f03cfc6 |
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--- a/prokka.xml Thu Oct 01 14:14:06 2015 -0400 +++ b/prokka.xml Fri Oct 28 13:03:19 2016 -0400 @@ -1,162 +1,204 @@ -<tool id="prokka" name="Prokka" version="1.11.0"> - <description>prokaryotic genome annotation</description> - <requirements> - <requirement type="package" version="2.2.31">blast+</requirement> - <requirement type="package" version="3.1b2">hmmer</requirement> - <requirement type="package" version="1.2.36">aragorn</requirement> - <requirement type="package" version="2.60">prodigal</requirement> - <requirement type="package" version="24.3">tbl2asn</requirement> - <requirement type="package" version="20131122">gnu_parallel</requirement> - <requirement type="package" version="0.7">barrnap</requirement> - <requirement type="package" version="1.1">infernal</requirement> - <requirement type="package" version="0.1.6">minced</requirement> - <requirement type="package" version="1.11">prokka</requirement> - </requirements> - <version_command>prokka --version</version_command> - <command> - 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 +<tool id="prokka" name="Prokka" version="1.11.1"> + <description>prokaryotic genome annotation</description> + <requirements> + <requirement type="package" version="1.11">prokka</requirement> + </requirements> + <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> + <stdio> + <exit_code range="1:" /> + </stdio> + <version_command>prokka --version</version_command> + <command><![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 $notrna - --notrna + #if str($compliant.mincontig) + --mincontig $compliant.mincontig #end if - $input - </command> - <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> - <stdio> - <exit_code range="1:" /> - </stdio> - <inputs> - <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> - <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" /> - <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)"> - <validator type="in_range" min="1" /> - </param> - <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" optional="true" label="Similarity e-value cut-off"> - <validator type="in_range" min="0" /> - </param> - <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" /> - </inputs> - <outputs> - <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff" /> - <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk" /> - <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna" /> - <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa" /> - <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn" /> - <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn" /> - <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa" /> - <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl" /> - <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err" /> - <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt" /> - <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" /> - </outputs> - <help> +#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="PROKKA" 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" label="Additional outputs"> + <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations</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</option> + <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences</option> + <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences</option> + <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS</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.</option> + <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines</option> + <option value="tbl" selected="True">Feature Table file</option> + <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report</option> + <option value="txt" selected="True">Statistics relating to the annotated features found</option> + </param> + + </inputs> + <outputs> + <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff"> + <filter>'gff' in outputs</filter> + </data> + <data name="out_gbk" format="txt" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk"> + <filter>'gbk' in outputs</filter> + </data> + <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna"> + <filter>'fna' in outputs</filter> + </data> + <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa"> + <filter>'faa' in outputs</filter> + </data> + <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn"> + <filter>'ffn' in outputs</filter> + </data> + <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn"> + <filter>'sqn' in outputs</filter> + </data> + <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa"> + <filter>'fsa' in outputs</filter> + </data> + <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl"> + <filter>'tbl' in outputs</filter> + </data> + <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err"> + <filter>'err' in outputs</filter> + </data> + <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt"> + <filter>'txt' in outputs</filter> + </data> + <data name="out_log" format="txt" label="${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,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.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. @@ -192,17 +234,18 @@ **License and citation** -This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ -.. _MIT license: http://opensource.org/licenses/MIT +.. _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://www.vicbioinformatics.com/software.prokka.shtml - </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btu135</citation> - <citation type="doi">10.1093/bioinformatics/btu153</citation> - </citations> + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu135</citation> + <citation type="doi">10.1093/bioinformatics/btu153</citation> + </citations> </tool>