comparison prokka.xml @ 14:eaee459f3d69 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f

13:a17498c603ec

<tool id="prokka" name="Prokka" version="1.12.0">
    <description>prokaryotic genome annotation</description>
    <requirements>
        <requirement type="package" version="1.12">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

#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>

            <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="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>

        <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 ${on_string}: tbl" from_work_dir="outdir/prokka.tbl">
             <filter>outputs and 'tbl' in outputs</filter>
        </data>
        <data name="out_err" format="txt" label="${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">

        <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." />

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`_ 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

14:eaee459f3d69

<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

#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>

            <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>

        <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">

        <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." />

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