Mercurial > repos > ecology > sanntis_marine
changeset 1:9d689f8c9ce4 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics commit 9dff0476530d65342db00896f3108edb899e3fd2
| author | ecology |
|---|---|
| date | Thu, 08 Aug 2024 11:58:48 +0000 |
| parents | 12870a79d56b |
| children | |
| files | sanntis.xml test-data/BGC0001472.fna test-data/Regex_Find_And_Replace_on_data_21.fasta test-data/Sanntis_output_data.genbank |
| diffstat | 4 files changed, 637 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/sanntis.xml Fri Jul 26 14:31:32 2024 +0000 +++ b/sanntis.xml Thu Aug 08 11:58:48 2024 +0000 @@ -2,7 +2,7 @@ <description>in genomic and metagenomic data</description> <macros> <token name="@TOOL_VERSION@">0.9.3.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <edam_topics> <edam_topic>topic_3387</edam_topic> @@ -11,21 +11,49 @@ <requirement type="package" version="@TOOL_VERSION@">sanntis</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - sanntis --ip-file '$input_interpro' --outfile 'output_sanntis.gff' '$input_genbank' + #if $selection.which_sanntis == 'sanntis': + sanntis --ip-file '$selection.input_interpro' --outfile 'output_sanntis.gff' '$selection.input_genbank' + #else: + sanntis_build_gb -n '$selection.input_nuc' -a '$selection.input_prot' -o 'output_sanntis_gb.gb' + #end if ]]></command> <inputs> - <param name="input_interpro" type="data" format="tabular" label="Input the TSV file from InterProScan" help="Before using this tool you need to retrieve the right data by using the InterProScan tool"/> - <param name="input_genbank" type="data" format="genbank" label="Input a Genbank .gb file" help="It needs to have the right structure and fit the protein fasta file used in InterProScan"/> + <conditional name="selection"> + <param name="which_sanntis" type="select" label="Do you want to build a genbank or to make a SMBGC Annotation?" help="If you decide to build a genbank you can then use this genbank to then conduct the annotation."> + <option value="sanntis">Run sanntis</option> + <option value="genbank">Build genbank</option> + </param> + <when value="sanntis"> + <param name="input_interpro" type="data" format="tabular" label="Input the tabular file from InterProScan" help="Before using this tool you need to retrieve the right data by using the InterProScan tool"/> + <param name="input_genbank" type="data" format="genbank" label="Input a Genbank file" help="It needs to have the right structure and fit the protein fasta file used in InterProScan"/> + </when> + <when value="genbank"> + <param name="input_nuc" type="data" format="fasta" label="Input a nucleotide fasta file"/> + <param name="input_prot" type="data" format="fasta" label="Input a protein fasta file" help="Before using this tool you can get the right protein data by using the Prodigal tool"/> + </when> + </conditional> </inputs> <outputs> - <data name="output_sanntis" from_work_dir="output_sanntis.gff" format="gff3" label="Sanntis output data"/> + <data name="output_sanntis" from_work_dir="output_sanntis.gff" format="gff3" label="Sanntis output data"> + <filter>selection['which_sanntis'] == 'sanntis'</filter> + </data> + <data name="output_sanntis_gb" from_work_dir="output_sanntis_gb.gb" format="genbank" label="Sanntis output data genbank"> + <filter>selection['which_sanntis'] == 'genbank'</filter> + </data> </outputs> <tests> <test expect_num_outputs="1"> + <param name="which_sanntis" value="sanntis"/> <param name="input_interpro" value="BGC0001472.fna.prodigal.faa.ip.tsv"/> <param name="input_genbank" value="BGC0001472.fna.prodigal.faa.gb"/> <output name="output_sanntis" value="Sanntis_output_data.gff3"/> </test> + <test expect_num_outputs="1"> + <param name="which_sanntis" value="genbank"/> + <param name="input_nuc" value="BGC0001472.fna"/> + <param name="input_prot" value="Regex_Find_And_Replace_on_data_21.fasta"/> + <output name="output_sanntis_gb" value="Sanntis_output_data.genbank"/> + </test> </tests> <help><