Mercurial > repos > crs4 > prokka

changeset 12:720f2d10ae39 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c"
author iuc
date Tue, 16 Nov 2021 18:58:50 +0000
parents bcb54922f85c
children
files prokka.xml prokka.xml.orig
diffstat 2 files changed, 12 insertions(+), 263 deletions(-) [+]
line wrap: on
line diff
--- a/prokka.xml	Wed Sep 01 08:15:56 2021 +0000
+++ b/prokka.xml	Tue Nov 16 18:58:50 2021 +0000
@@ -5,7 +5,7 @@
     </xrefs>
     <macros>
         <token name="@TOOL_VERSION@">1.14.6</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">prokka</requirement>
@@ -135,7 +135,7 @@
         <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">
+        <param name="outputs" type="select" multiple="true" 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>
@@ -151,7 +151,7 @@
 
     </inputs>
     <outputs>
-        <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff">
+        <data name="out_gff" format="gff3" label="${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">
@@ -190,27 +190,27 @@
         <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_gff" file="out.gff" ftype="gff3" />
             <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_fna" file="out.fna" ftype="fasta" />
+            <output name="out_faa" file="out.faa" ftype="fasta" />
+            <output name="out_ffn" file="out.ffn" ftype="fasta" />
             <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_fsa" file="out.fsa" ftype="fasta" />
+            <output name="out_tbl" file="out.tbl" ftype="txt" />
+            <output name="out_tsv" file="out.tsv" ftype="tabular" />
+            <output name="out_err" file="out.err" lines_diff="14" ftype="txt" />
+            <output name="out_txt" file="out.txt" ftype="txt" />
             <output name="out_log">
                 <assert_contents>
                     <has_text text="Type 'prokka --citation' for more details." />
--- a/prokka.xml.orig	Wed Sep 01 08:15:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,251 +0,0 @@
-<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>