comparison antismash.xml @ 4:e78e25d3b4bd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit f5f8e44e726c9f2cc57e0f0fe8182a73afa56669

3:5784e268efca

<?xml version='1.0' encoding='utf-8'?>
<tool id="antismash" name="Antismash" version="5.1.2" profile="17.01">
    <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>
    <requirements>
        <requirement type="package" version="5.1.2">antismash</requirement>
    </requirements>
    <version_command>antismash --version</version_command>
    <command detect_errors="aggressive">
<![CDATA[
        export PYTHONWARNINGS="ignore::FutureWarning" &&

        #else:
            #set $file_extension = $infile.ext
        #end if

        ln -s '$infile' input_tempfile.$file_extension &&

        ## create html folder
        mkdir -p '$htmloutputfolder' &&

        antismash
            --cpus "\${GALAXY_SLOTS:-12}"
            --taxon '${cond_taxon.taxon}'

            --genefinding-tool $cond_taxon.genefinding_tool

            ${cb_general}
            ${cb_subclusters}
            ${cb_knownclusters}
            ${smcog_trees}
            --tta-threshold ${tta_threshold}
            ${asf}

            ${extra_cluster}
            ${clusterhmmer}
            ${fullhmmer}
            #if $cond_taxon.taxon == 'fungi':
                $cond_taxon.cassis
            #end if

            input_tempfile.$file_extension &&

        ## copy all content to html folder
        cp input_tempfile/index.html '${html}' 2> /dev/null &&
        cp -r input_tempfile/* '${htmloutputfolder}'

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/>

        <conditional name="cond_taxon">
            <param argument="--taxon" type="select" label="Origin of DNA">
                <option value="bacteria" selected="True">Bacteria</option>
                <option value="fungi">Fungi</option>
            </param>
            <when value="bacteria">
                <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"
                    help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding">
                    <option value="prodigal" selected="True">Prodigal</option>
                    <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option>
                    <option value="glimmerhmm">GlimmerHMM</option>
                    <option value="none">None</option>
                    <option value="error">Error</option>
                </param>
            </when>
            <when value="fungi">
                <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding"
                    help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding">
                    <option value="glimmerhmm">GlimmerHMM</option>
                    <option value="none">None</option>
                    <option value="error">Error</option>
                </param>
                <param argument="--cassis" type="boolean" truevalue="--cassis" falsevalue="" checked="False"
                       label="Motif based prediction of SM gene cluster regions" />
            </when>
        </conditional>


        <param argument="--cb-general" type="boolean" truevalue="--cb-general" falsevalue="" checked="False"
               label="BLAST identified clusters against known clusters"
               help="Compare identified clusters against a database of antiSMASH-predicted clusters." />
        <param argument="--cb-subclusters" type="boolean" truevalue="--cb-subclusters" falsevalue="" checked="True"
               label="Subcluster BLAST analysis"
               help="Compare identified clusters against known subclusters responsible for synthesising precursors." />
        <param argument="--cb-knownclusters" type="boolean" truevalue="--cb-knownclusters" falsevalue="" checked="True"
               label="KnowCluster BLAST analysis"
               help="Compare identified clusters against known gene clusters from the MIBiG database."/>
        <param argument="--smcog-trees" type="boolean" checked="True" truevalue="--smcog-trees" falsevalue=""
               label="Analysis of secondary metabolism gene families (smCOGs)"
               help="Look for sec. met. clusters of orthologous groups."/>
        <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True"
               label="Run active site finder analysus" />
        <param argument="-pfam2go" type="boolean" truevalue="-pfam2go" falsevalue="" checked="True"
               label="Run Pfam to Gene Ontology mapping module" />
        <param argument="--tta-threshold" type="float" value="0.65" label="Lowest GC content to annotate TTA codons at" />

        <param argument="--clusterhmmer" type="boolean" truevalue="--clusterhmmer" falsevalue="" checked="False"
               label="Run a cluster-limited HMMer analysis" />
        <param argument="--fullhmmer" type="boolean" truevalue="--fullhmmer" falsevalue="" checked="False"
               label="Run a whole-genome HMMer analysis" />

        <param name="extra_cluster" type="select" label="Clusters">
            <option value="--cf-create-clusters" selected="True">Find extra clusters</option>
            <option value="--cf-borders-only">Only annotate borders of existing clusters</option>
        </param>

        <param name="outputs" type="select" multiple="true" label="Outputs">
            <option value="html" selected="True">HTML file</option>
            <option value="all">All results</option>
            <option value="embl">EMBL files</option>
            <option value="gb">GenBank files</option>
            <option value="genecluster_tabular">Gene clusters</option>
        </param>

    </inputs>
    <outputs>
        <collection type="list" name="genecluster_tabular" label="${tool.name} on ${on_string} (Gene Cluster)">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.txt" directory="input_tempfile" ext="txt" visible="false" />
            <filter>'genecluster_tabular' in outputs</filter>
        </collection>
        <collection name="genbank" type="list" label="${tool.name} on ${on_string} (GenBank)">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="genbank" visible="false" />
            <filter>'gb' in outputs</filter>
        </collection>
        <collection name="embl" type="list" label="${tool.name} on ${on_string} (EMBL)">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="embl" visible="false" />
            <filter>'embl' in outputs</filter>
        </collection>
        <collection name="archive" type="list" label="${tool.name} on ${on_string} (all files compressed)">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.zip" directory="input_tempfile" ext="zip" visible="false" />
            <filter>'all' in outputs</filter>
        </collection>
        <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="sequence.fasta"/>
            <output name="html" file="index.html"/>
        </test>
        <test>
            <param name="infile" value="sequence.gb"/>
            <param name="outputs" value="html,gb"/>
            <param name="taxon" value="fungi"/>
            <param name="clusterhmmer" value="True"/>
            <param name="fullhmmer" value="True"/>
            <param name="extra_cluster" value="--cf-create-clusters"/>
            <param name="cassis" value="True"/>
            <param name="cb_general" value="True"/>
            <output_collection name="genbank" type="list">
                <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" />
                <element name="ARBH01000003.1.final" file="ARBH01000003.1.final" ftype="genbank"/>
            </output_collection>
            <output name="html" file="index.2.html"/>
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

The downward-pointing arrow will open a menu offering to download the complete set of results from the antiSMASH run, a summary Excel file and to the summary EMBL/GenBank output file.
The EMBL/GenBank file can be viewed in a genome browser such as Artemis.

]]>
    </help>
    <citations>
        <citation type="doi">10.1093/nar/gkv437</citation>
    </citations>
</tool>

4:e78e25d3b4bd

<tool id="antismash" name="Antismash" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='requirements'/>
    <expand macro="bio_tools"/>
    <version_command>antismash --version</version_command>
    <command detect_errors="aggressive">
<![CDATA[
        export PYTHONWARNINGS="ignore::FutureWarning" &&

        #else:
            #set $file_extension = $infile.ext
        #end if

        ln -s '$infile' input_tempfile.$file_extension &&
        #if $genefinding_gff3
            ln -s $genefinding_gff3 annotation.gff3 &&
        #end if


        ## create html folder
        mkdir -p '$htmloutputfolder' &&

        antismash
            --cpus "\${GALAXY_SLOTS:-12}"
            --taxon '${cond_taxon.taxon}'
            #if $genefinding_gff3
                --genefinding-gff3 annotation.gff3
            #end if
            --genefinding-tool $cond_taxon.genefinding_tool

            ${cb_general}
            ${cb_subclusters}
            ${cb_knownclusters}
            ${smcog_trees}
            --tta-threshold ${tta_threshold}
            ${asf}

            ${clusterhmmer}
            ${fullhmmer}
            #if $cond_taxon.taxon == 'fungi':
                $cond_taxon.cassis
            #else   
                $cond_taxon.tigrfam
            #end if

            ${cc_mibig}
            ${rre}
            --logfile $log

            ## Advanced options
            --minlength $advanced_options.minlength
            --hmmdetection-strictness $advanced_options.hmmdetection_strictness
            --cb-nclusters $advanced_options.cb_nclusters
            --cb-min-homology-scale $advanced_options.cb_min_homology_scale
            --rre-cutoff $advanced_options.rre_cutoff
            --rre-minlength $advanced_options.rre_minlength

            input_tempfile.$file_extension &&

        ## copy all content to html folder
        cp input_tempfile/index.html '${html}' 2> /dev/null &&
        cp -r input_tempfile/* '${htmloutputfolder}'
]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/>
        <param argument="--genefinding-gff3" type="data" format="gff3" optional="true" label="GFF3 file" help="Specify GFF3 file to extract features from" />

        <conditional name="cond_taxon">
            <param argument="--taxon" type="select" label="Taxonomic classification of input sequence" help="Source of DNA">
                <option value="bacteria" selected="True">Bacteria</option>
                <option value="fungi">Fungi</option>
            </param>
            <when value="bacteria">
                <expand macro="genefinding">
                    <option value="prodigal" selected="True">Prodigal</option>
                    <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option>
                </expand>
                <param argument="--tigrfam" type="boolean" truevalue="--tigrfam" falsevalue="" checked="false" 
                    label="Annotate with TIGRFam" help="Annotate clusters using TIGRFam profiles. TIGRFAMs is a 
                    collection of manually curated protein families focusing primarily on prokaryotic sequences" />
            </when>
            <when value="fungi">
                <expand macro="genefinding"/>
                <param argument="--cassis" type="boolean" truevalue="--cassis" falsevalue="" checked="false"
                       label="Motif based prediction of SM gene cluster regions" help="Improved prediction of gene cluster borders for fungal BGCs (CASSIS)"/>
            </when>
        </conditional>
        <param argument="--fullhmmer" type="boolean" truevalue="--fullhmmer" falsevalue="" checked="false"
            label="Full genome PFAM anotation"  help="Each gene product encoded in the detected BGCs is analyzed against the PFAM database. 
                Hits are annotated in the final Genbank/EMBL files. Also, selecting this option normally increases the runtime"/>
        
        <param argument="--clusterhmmer" type="boolean" truevalue="--clusterhmmer" falsevalue="" checked="false"
            label="PFAM anotation for only clusters" help="Run a cluster-limited HMMer analysis" />

        <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True"
            label="Run active site finder analysis" help="Active sites of several highly conserved biosynthetic enzymes are detected and variations of the active sites are reported"/>

        <param argument="--cc-mibig" type="boolean" truevalue="--cc-mibig" falsevalue="" checked="false" label="Comparison against MIBiG database" help="Run a comparison against the MIBiG database" />

        <param argument="--cb-general" type="boolean" truevalue="--cb-general" falsevalue="" checked="false"
            label="BLAST identified clusters against known clusters"
            help="Compare identified clusters against a database of antiSMASH-predicted clusters." />

        <param argument="--cb-knownclusters" type="boolean" truevalue="--cb-knownclusters" falsevalue="" checked="true"
            label="KnowCluster BLAST analysis"
            help="Compare identified clusters against known gene clusters from the MIBiG database. MIBiG is a hand curated data collection of biosynthetic 
                gene clusters, which have been experimentally characterized"/>

        <param argument="--cb-subclusters" type="boolean" truevalue="--cb-subclusters" falsevalue="" checked="true"
            label="Subcluster BLAST analysis"
            help="The identified clusters are searched against a database containing operons involved in the biosynthesis of common secondary metabolite building 
                blocks (e.g. the biosynthesis of non-proteinogenic amino acids)" />

        <param argument="--pfam2go" type="boolean" truevalue="--pfam2go" falsevalue="" checked="true"
            label="Run Pfam to Gene Ontology mapping module" />

        <param argument="--rre" type="boolean" truevalue="--rre" falsevalue="" checked="true" label="RREFinder precision mode" help="Run RREFinder precision mode on all RiPP gene clusters. Many ribosomally 
            synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs 
            the posttranslational modification enzymes to their substrates" />

        <param argument="--smcog-trees" type="boolean" checked="True" truevalue="--smcog-trees" falsevalue=""
            label="Analysis of secondary metabolism gene families (smCOGs)"
            help="It attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene family using profile hidden Markov models specific for 
                the conserved sequence region characteristic of this family. In other words, each gene of the cluster is compared to a database of clusters of orthologous groups 
                of proteins involved in secondary metabolism"/>

        <param argument="--tta-threshold" type="float" value="0.65" label="Lowest GC content to annotate TTA codons at" 
            help="High-GC containing bacterial sequences contain the rare Leu-codon “TTA” as a mean for post-transcriptional regulation by limiting/controlling the amount of TTA-tNRA in the cell. 
                This type of regulation is commonly found in secondary metabolite BGCs. This feature will annotate such TTA codons in the identified BGCs. Default: 0.65"/>
        <section name="advanced_options" title="Advanced options">
            <param argument="--minlength" type="integer" min="0" value="1000" label="Min length" help="Only process sequences larger than this value. Default: 1000" />
            <param argument="--hmmdetection-strictness" type="select" label="HMM detection strictness" help="Defines which level of strictness to use for HMM-based cluster detection. Default: relaxed">
                <option value="strict">Strict</option>
                <option value="relaxed" selected="true">Relaxed</option>
                <option value="loose">Loose</option>
            </param>
            <param argument="--cb-nclusters" type="integer" min="0" max="50" value="10" label="Number of clusters from ClusterBlast to display" help="Default: 10" />
            <param argument="--cb-min-homology-scale" type="float" min="0" max="1" value="0" label="ClusterBlast minimum scaling factor" help="A minimum scaling factor 
                for the query BGC in ClusterBlast results. Default: 0" />
            <param argument="--rre-cutoff" type="float" min="0" max="100" value="25" label="RRE cutoff" help="Bitscore cutoff for RRE pHMM detection. Default: 25.0" />
            <param argument="--rre-minlength" type="integer" min="0" max="100" value="50" label="RRE minlength" help="Minimum amino acid length of RRE domains. Default: 50" />
        </section>

        <param name="outputs" type="select" multiple="true" label="Outputs">
            <option value="html" selected="True">HTML file</option>
            <option value="all">All results</option>
            <option value="embl">EMBL files</option>
            <option value="gb">GenBank files</option>
            <option value="genecluster_tabular">Gene clusters</option>
            <option value="log">Log file</option>
        </param>

    </inputs>
    <outputs>
        <collection type="list" name="genecluster_tabular" label="${tool.name} on ${on_string}: Gene Cluster">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.txt" directory="input_tempfile" ext="txt" visible="false" />
            <filter>'genecluster_tabular' in outputs</filter>
        </collection>
        <collection name="genbank" type="list" label="${tool.name} on ${on_string}: GenBank">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="genbank" visible="false" />
            <filter>'gb' in outputs or fullhmmer</filter>
        </collection>
        <collection name="embl" type="list" label="${tool.name} on ${on_string}: EMBL">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" directory="input_tempfile" ext="embl" visible="false" />
            <filter>'embl' in outputs</filter>
        </collection>
        <collection name="archive" type="list" label="${tool.name} on ${on_string}: all files compressed">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.zip" directory="input_tempfile" ext="zip" visible="false" />
            <filter>'all' in outputs</filter>
        </collection>
        <data format="html" name="html" label="${tool.name} on ${on_string}: HTML report" />
        <data format="txt" name="log" label="${tool.name} on ${on_string}: log file">
            <filter>'log' in outputs</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="infile" value="sequence.fasta"/>
            <output name="html" file="index.html"/>
        </test>
        <test expect_num_outputs="2">
            <param name="infile" value="sequence.gb"/>
            <param name="outputs" value="html,gb"/>
            <param name="taxon" value="fungi"/>
            <param name="clusterhmmer" value="true"/>
            <param name="fullhmmer" value="true"/>
            <param name="cassis" value="true"/>
            <param name="cb_general" value="true"/>
            <output_collection name="genbank" type="list">
                <element name="input_tempfile" file="test_02.genbank" ftype="genbank" lines_diff="2"/>
            </output_collection>
            <output name="html" file="index.2.html" ftype="html">
                <assert_contents>
                    <has_text text="No results found on input"/>
                </assert_contents>
            </output>
        </test>

    <test expect_num_outputs="3">
        <param name="infile" value="sequence_long.fasta"/>
        <param name="genefinding_gff3" value="annotation.gff3"/>
        <param name="fullhmmer" value="true"/>
        <param name="cc_mibig" value="true"/>
        <param name="pfam2go" value="true"/>
        <param name="rre" value="true"/>
        <param name="outputs" value="html,gb,log"/>
        <section name="advanced_options">
            <param name="minlength" value="1000"/>
            <param name="hmmdetection_strictness" value="strict"/>
            <param name="cb_nclusters" value="10"/>
            <param name="cb_min_homology_scale" value="0.1"/>
            <param name="rre_cutoff" value="10"/>
            <param name="rre_minlength" value="50"/>
        </section>
        <output_collection name="genbank" type="list">
            <element name="input_tempfile" file="test_03.genbank" ftype="genbank" lines_diff="2"/>
        </output_collection>
        <output name="html" file="index.3.html" ftype="html">
            <assert_contents>
                <has_text text="No results found on input"/>
            </assert_contents>
        </output>
        <output name="log">
            <assert_contents>
                <has_text text="antiSMASH status: SUCCESS"/>
                <has_text text="HMM detection using strictness: strict"/>
            </assert_contents>
        </output>
    </test>
 
    </tests>
    <help>
<![CDATA[

**What it does**

The downward-pointing arrow will open a menu offering to download the complete set of results from the antiSMASH run, a summary Excel file and to the summary EMBL/GenBank output file.
The EMBL/GenBank file can be viewed in a genome browser such as Artemis.

]]>
    </help>
    <expand macro="citations" />
</tool>