Mercurial > repos > crs4 > prokka
changeset 11:bcb54922f85c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 08:15:56 +0000 |
| parents | f0fffaf68f1c |
| children | 720f2d10ae39 |
| files | prokka.xml prokka.xml.orig |
| diffstat | 2 files changed, 254 insertions(+), 0 deletions(-) [+] |
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--- a/prokka.xml Sat Feb 13 11:58:02 2021 +0000 +++ b/prokka.xml Wed Sep 01 08:15:56 2021 +0000 @@ -1,5 +1,8 @@ <tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Prokaryotic genome annotation</description> + <xrefs> + <xref type="bio.tools">prokka</xref> + </xrefs> <macros> <token name="@TOOL_VERSION@">1.14.6</token> <token name="@VERSION_SUFFIX@">0</token>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prokka.xml.orig Wed Sep 01 08:15:56 2021 +0000 @@ -0,0 +1,251 @@ +<tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>Prokaryotic genome annotation</description> +<<<<<<< HEAD + <macros> + <token name="@TOOL_VERSION@">1.14.6</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> +======= + <xrefs> + <xref type='bio.tools'>prokka</xref> + </xrefs> +>>>>>>> 7abad681f (add tools up until P) + <requirements> + <requirement type="package" version="@TOOL_VERSION@">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 argument="--locustag" type="text" value="" label="Locus tag prefix" /> + <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" /> + <param argument="--gffver" type="select" label="GFF version"> + <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" + help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)"> + <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 argument="--centre" type="text" value="" label="Sequencing centre ID" /> + <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" /> + <param argument="--species" type="text" value="" label="Species name" /> + <param argument="--strain" type="text" value="" label="Strain name" /> + <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" /> + <conditional name="kingdom"> + <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)"> + <option value="Archaea">Archaea</option> + <option value="Bacteria" selected="true">Bacteria</option> + <option value="Viruses">Viruses</option> + </param> + <when value="Archaea"> + <param argument="--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 argument="--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 argument="--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 argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" /> + <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" /> + <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" /> + <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" /> + <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" /> + <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" /> + <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> + <param argument="--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" > + <assert_contents> + <has_text_matching expression="LOCUS" /> + <has_text_matching expression="//" /> + </assert_contents> + </output> + <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" > + <assert_contents> + <has_text_matching expression="Seq-entry" /> + <has_text_matching expression="contig2" /> + </assert_contents> + </output> + <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" lines_diff="14" /> + <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>