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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
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0:12870a79d56b 1:9d689f8c9ce4
1 <tool id="sanntis_marine" name="Sanntis biosynthetic gene clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> 1 <tool id="sanntis_marine" name="Sanntis biosynthetic gene clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description>in genomic and metagenomic data</description> 2 <description>in genomic and metagenomic data</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.9.3.5</token> 4 <token name="@TOOL_VERSION@">0.9.3.5</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <edam_topics> 7 <edam_topics>
8 <edam_topic>topic_3387</edam_topic> 8 <edam_topic>topic_3387</edam_topic>
9 </edam_topics> 9 </edam_topics>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">sanntis</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">sanntis</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 sanntis --ip-file '$input_interpro' --outfile 'output_sanntis.gff' '$input_genbank' 14 #if $selection.which_sanntis == 'sanntis':
15 sanntis --ip-file '$selection.input_interpro' --outfile 'output_sanntis.gff' '$selection.input_genbank'
16 #else:
17 sanntis_build_gb -n '$selection.input_nuc' -a '$selection.input_prot' -o 'output_sanntis_gb.gb'
18 #end if
15 ]]></command> 19 ]]></command>
16 <inputs> 20 <inputs>
17 <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"/> 21 <conditional name="selection">
18 <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"/> 22 <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.">
23 <option value="sanntis">Run sanntis</option>
24 <option value="genbank">Build genbank</option>
25 </param>
26 <when value="sanntis">
27 <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"/>
28 <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"/>
29 </when>
30 <when value="genbank">
31 <param name="input_nuc" type="data" format="fasta" label="Input a nucleotide fasta file"/>
32 <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"/>
33 </when>
34 </conditional>
19 </inputs> 35 </inputs>
20 <outputs> 36 <outputs>
21 <data name="output_sanntis" from_work_dir="output_sanntis.gff" format="gff3" label="Sanntis output data"/> 37 <data name="output_sanntis" from_work_dir="output_sanntis.gff" format="gff3" label="Sanntis output data">
38 <filter>selection['which_sanntis'] == 'sanntis'</filter>
39 </data>
40 <data name="output_sanntis_gb" from_work_dir="output_sanntis_gb.gb" format="genbank" label="Sanntis output data genbank">
41 <filter>selection['which_sanntis'] == 'genbank'</filter>
42 </data>
22 </outputs> 43 </outputs>
23 <tests> 44 <tests>
24 <test expect_num_outputs="1"> 45 <test expect_num_outputs="1">
46 <param name="which_sanntis" value="sanntis"/>
25 <param name="input_interpro" value="BGC0001472.fna.prodigal.faa.ip.tsv"/> 47 <param name="input_interpro" value="BGC0001472.fna.prodigal.faa.ip.tsv"/>
26 <param name="input_genbank" value="BGC0001472.fna.prodigal.faa.gb"/> 48 <param name="input_genbank" value="BGC0001472.fna.prodigal.faa.gb"/>
27 <output name="output_sanntis" value="Sanntis_output_data.gff3"/> 49 <output name="output_sanntis" value="Sanntis_output_data.gff3"/>
50 </test>
51 <test expect_num_outputs="1">
52 <param name="which_sanntis" value="genbank"/>
53 <param name="input_nuc" value="BGC0001472.fna"/>
54 <param name="input_prot" value="Regex_Find_And_Replace_on_data_21.fasta"/>
55 <output name="output_sanntis_gb" value="Sanntis_output_data.genbank"/>
28 </test> 56 </test>
29 </tests> 57 </tests>
30 <help><![CDATA[ 58 <help><![CDATA[
31 59
32 .. class:: infomark 60 .. class:: infomark
33 61
34 **What it does** 62 **What it does**
35 63
36 SMBGC Annotation using Neural Networks Trained on Interpro Signatures 64 SMBGC Annotation using Neural Networks Trained on Interpro Signatures
37 Tool for identifying biosynthetic gene clusters (BGCs) in genomic & metagenomic data 65 Tool for identifying biosynthetic gene clusters (BGCs) in genomic & metagenomic data
66
67 **Or**
68
69 This tool can also create a Genbank adapted to be used in sanntis
38 70
39 ..... 71 .....
40 72
41 73
42 **Input** 74 **Input**