| Previous changeset 18:d643e3b03500 (2021-02-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 3c234f3dbee389d82b065d9c685818f86838017c" |
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modified:
prokka.xml |
| b |
| diff -r d643e3b03500 -r 8a22554cdde2 prokka.xml --- a/prokka.xml Sat Feb 13 11:58:58 2021 +0000 +++ b/prokka.xml Tue Nov 16 18:59:22 2021 +0000 |
| b |
| @@ -1,8 +1,11 @@ <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> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">prokka</requirement> @@ -132,7 +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> @@ -148,7 +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"> @@ -187,27 +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." /> |