annotate motus_profiler.xml @ 0:d20f3b9a59a2 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mOTUs commit 36fa40d4507065b7240c0a98815a079aba589e25

<tool id="motus_profiler" name="mOTUs_profiler" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>performs taxonomic profiling of metagenomics and metatrancriptomics samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[   
        #if $db.db_source == 'cached'
            #set $DATABASE_DIR=$db.db_cached.fields.path
        #else
            #set $database_path = $db.database
            mkdir database_dir &&
            tar -xvf '$database_path' -C database_dir/ &&
            #set $DATABASE_DIR = 'database_dir/db_mOTU' ##the actual DB folder in the archive called db_mOTU
        #end if
        echo "Database Directory:" $DATABASE_DIR  &&

        motus profile 
        -t \${GALAXY_SLOTS:-8} 
        -n '$sample_name' 
        -db '$DATABASE_DIR'
        #if $inputs.input_type.selector == 'reads'
            #if $inputs.input_type.reads_type.selector == 'paired'
                -f '${inputs.input_type.reads_type.forward_reads}' 
                -r '${inputs.input_type.reads_type.reverse_reads}'
            #elif $inputs.input_type.reads_type.selector == 'single'
                -s '${inputs.input_type.reads_type.unpaired_reads}'   
            #elif $input_type.selector == 'SAM_BAM_input'
                -i '${inputs.input_type.SAM_BAM_input}'
            #elif $input_type.selector == 'mgc_read_count'
                -m '${inputs.input_type.mgc_read_count}'
            #end if
        #end if
        #if $algorithm_advanced_options.advanced_options.customize_algorithm_options == 'customize'
            -g $algorithm_advanced_options.advanced_options.marker_genes_cutoff
            -l $algorithm_advanced_options.advanced_options.minimum_alignment_len
            -v $algorithm_advanced_options.advanced_options.verbosity_level_selection
            -y $algorithm_advanced_options.advanced_options.read_count_type_selection
        #end if
        
        #if $biom_format
        -o '$output_biom'
        $biom_format
        #elif $ref_motus
        -o '$output_ref'
        $ref_motus
        #elif $full_species_name
        -o '$output_species'
        $full_species_name
        #elif $result_as_counts
        -o '$output_counts'
        $result_as_counts
        #elif $ncbi_taxonomy_ids
        -o '$output_ncbi'
        $ncbi_taxonomy_ids
        #elif $full_rank_taxonomy
        -o '$output_fullrank'
        $full_rank_taxonomy
        #elif $all_taxonomic_level
        -o '$output_alltaxonomy'
        $all_taxonomic_level

        #elif $cami_format_option.cami_options == 'yes'
        -o '$output_cami'
        -C $cami_format_option.cami_format
        #elif $taxonomic_level_option.taxonomic_option == 'yes'
        -o '$output_taxonomic'
        -k $taxonomic_level_option.taxonomic_level
        #else
        -o '$output_motus'
        #end if
        #if $save_bam
        -I '$output_bam'
        #end if
        #if $save_mgc
        -M '$output_mgc'
        #end if

    ]]></command>
    <inputs>
        <section name="inputs" title="Inputs" expanded="true">
            <conditional name="input_type">
                <param name="selector" type="select" label="Input file(s)">
                    <option value="reads" selected="True">fastq,fastq.gz file(s)</option>
                    <option value="SAM_BAM_input">SAM/BAM input file(s) generated by motus map_tax</option>
                    <option value="mgc_read_count">mgc_read_count file(s) generated by motus cal-mgc</option>
                </param>
                <when value="reads">
                    <conditional name="reads_type">
                        <param name="selector" type="select" format="fastq,fastq.gz" label="Choose input file(s)">
                            <option value="paired">Paired-end</option>
                            <option value="single" selected="true">Single</option>
                        </param>
                        <when value="paired">
                            <param name="forward_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="-f Input file(s) for reads in forward orientation, fastq(.gz)-formatted"/>
                            <param name="reverse_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="-r Input file(s) for reads in reverse orientation, fastq(.gz)-formatted"/>
                        </when>
                        <when value="single">
                            <param name="unpaired_reads" type="data" format="fastq,fastq.gz" label="Single reads" help="-s input file(s) for single reads, fastq(.gz)-formatted"/>
                        </when>
                    </conditional>
                </when>
                <when value="SAM_BAM_input">
                    <param name="SAM_BAM_input" type="data" format="sam,bam" label="motus map_tax SAM or BAM file" help="-i SAM or BAM input file(s) generated by motus map_tax"/>
                </when>
                <when value="mgc_read_count">
                    <param name="mgc_count" type="data" format="mgc" label="mgc read count file)(s)" help="-m mgc reads count file generated by motus calc_mgc"/>
                </when>
            </conditional>
            <param name="sample_name" type="text" label="Sample name" help="sample name can contain letters and/or numbers" default_value="unnamed sample"/>
            <conditional name="db">
                <param name="db_source" type="select" label="mOTUs Database">
                    <option value="cached" selected="True">Use a pre-installed database</option>
                    <option value="history">Use a database from history</option>
                </param>
                <when value="cached">
                    <param name="db_cached" type="select" label="A pre-installed mOTUs databese" help="no pre-installed mOTUs databases are avalable yet">
                        <options from_data_table="motus_db_versioned">
                            <filter type="sort_by" column="1"/>
                            <validator type="no_options" message="No compatible motus database is available"/>
                        </options>
                    </param>
                </when>
                <when value="history">
                    <param name="database" type="data" format="tar" label="Database from history" help="Custom database or other version of mOTUs database from link: https://zenodo.org/records/5140350"/>
                </when>
            </conditional>
        </section>
        <param argument="ref_motus" type="boolean" label="only species with reference genomes (ref-mOTUs)" truevalue="-e" falsevalue="" checked="false"/>
        <param argument="full_species_name" type="boolean" label="print the full name of the species" truevalue="-u" falsevalue="" checked="false"/>
        <param argument="result_as_counts" type="boolean" label="print result as counts" help="-c print result as counts instead of relative abundances." truevalue="-p" falsevalue="" checked="false"/>
        <param argument="ncbi_taxonomy_ids" type="boolean" label="print NCBI taxonomy identifiers" truevalue="-p" falsevalue="" checked="false"/>
        <param argument="biom_format" type="boolean" label="print result in BIOM format" truevalue="-B" falsevalue="" checked="false"/>
        <param argument="full_rank_taxonomy" type="boolean" label="print the full rank taxonomy" truevalue="-q" falsevalue="" checked="false"/>
        <param argument="all_taxonomic_level" type="boolean" label="print all taxonomic levels together" help="-A print all taxonomic levels together (kingdom to mOTUs, override -k)." truevalue="-A" falsevalue="" checked="false"/>
        <param argument="save_bam" type="boolean" label="BAM output" help="-I save the result of BWA in BAM format (output of motus map_tax)." truevalue="-I" falsevalue="" checked="false"/>
        <param argument="save_mgc" type="boolean" label="Mgc output" help="-M save the mgc reads count(output of motus calc_mgc)." truevalue="-M" falsevalue="" checked="false"/>
        <conditional name="cami_format_option">
            <param argument="cami_options" type="select" label="Choose cami_format">
                <option value="yes">yes</option>
                <option value="no" selected="True">no</option>
            </param>
            <when value="yes">
                <param argument="cami_format" type="select" label="Select value for cami format">
                    <option value="precision">Precision</option>
                    <option value="recall">Recall</option>
                    <option value="parenthesis">Parenthesis</option>
                </param>
            </when>
            <when value="no">
                <!-- Define actions or defaults for the default option if necessary -->
            </when>
        </conditional>
        <conditional name="taxonomic_level_option">
            <param argument="taxonomic_option" type="select" label="taxonomic_level">
                <option value="yes">yes</option>
                <option value="no" selected="True">no</option>
            </param>
            <when value="yes">
                <param argument="taxonomic_level" type="select" label="taxonomic_level">
                    <option value="kingdom">kingdom</option>
                    <option value="phylum">phylum</option>
                    <option value="class">class</option>
                    <option value="order">order</option>
                    <option value="family">family</option>
                    <option value="genus">genus</option>
                    <option value="mOTU" selected="True">default mOTU</option>
                </param>
            </when>
            <when value="no">
                <!-- Define actions or defaults for the default option if necessary -->
            </when>
        </conditional>
        <section name="algorithm_advanced_options" title="algorithm" expanded="true">
            <conditional name="advanced_options">
                <param argument="customize_algorithm_options" type="select" label="Advanced algorithm options">
                    <option value="default_options" selected="True">No, Use param defaults</option>
                    <option value="customize">Yes, See full parameter list</option>
                </param>
                <when value="customize">
                    <param argument="marker_genes_cutoff" type="select" label="Select number of marker genes cutoff" help="-g Select number of marker genes cutoff: 1=higher recall, 6=higher precision">
                        <option value="1">higher recall</option>
                        <option value="2">option 2</option>
                        <option value="3" selected="True">default option</option>
                        <option value="4">option 4</option>
                        <option value="5">option 5</option>
                        <option value="6">higher precision</option>
                    </param>
                    <param argument="minimum_alignment_len" type="integer" value="75" optional="true" label="Minimum Alignment Length (bp)" help="Specify the desired minimum alignment length in base pairs. Default value is 75bp."/>
                    <param argument="verbosity_level_selection" type="select" label="verbosity level" help="-v verbosity level: 1=error, 2=warning, 3=message, 4+=debugging">
                        <option value="1">error</option>
                        <option value="2">warning</option>
                        <option value="3" selected="True">message default</option>
                        <option value="4">debugging</option>
                    </param>
                    <param argument="read_count_type_selection" type="select" label="slect tyepe of read counts" help="-y type of read counts Values: [base.coverage, insert.raw_counts, insert.scaled_counts]">
                        <option value="base.coverage">base.coverage</option>
                        <option value="insert.raw_counts">insert.raw_counts</option>
                        <option value="insert.scaled_counts" selected="True">insert.scaled_counts default_value</option>
                    </param>
                </when>
                <when value="default_options">
                    <!-- Define actions or defaults for the default option if necessary -->
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="output_motus" format="txt" label="${tool.name} on ${on_string}: default Output">
            <filter>not biom_format and not ref_motus</filter>
        </data>
        <data name="output_biom" format="biom1" label="${tool.name} on ${on_string}: BIOM Output">
            <filter>biom_format</filter>
        </data>
        <data name="output_ref" format="txt" label="${tool.name} on ${on_string}: ref_motus Output">
            <filter>ref_motus</filter>
        </data>
        <data name="output_species" format="txt" label="${tool.name} on ${on_string}: species Output">
            <filter>full_species_name</filter>
        </data>
        <data name="output_counts" format="txt" label="${tool.name} on ${on_string}: count Output">
            <filter>result_as_counts</filter>
        </data>
        <data name="output_ncbi" format="txt" label="${tool.name} on ${on_string}: ncbi taxonomy Output">
            <filter>ncbi_taxonomy_ids</filter>
        </data>
        <data name="output_fullrank" format="txt" label="${tool.name} on ${on_string}: full rank taxonomy Output">
            <filter>full_rank_taxonomy</filter>
        </data>
        <data name="output_alltaxonomy" format="txt" label="${tool.name} on ${on_string}: all taxonomic level Output">
            <filter>all_taxonomic_level</filter>
        </data>
        <data name="output_bam" format="bam_no_index" label="${tool.name} on ${on_string}: BAM Output">
            <filter>save_bam</filter>
        </data>
        <data name="output_mgc" format="txt" label="${tool.name} on ${on_string}: mgc Output">
            <filter>save_mgc</filter>
        </data>
        <data name="output_cami" format="txt" label="${tool.name} on ${on_string}: cami Output">
            <filter>cami_format_option['cami_options']=="yes"</filter>
        </data>
        <data name="output_taxonomic" format="txt" label="${tool.name} on ${on_string}: taxonomic Output">
            <filter>taxonomic_level_option['taxonomic_option']=="yes"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="biom_format" value="false"/>
            <param name="ref_motus" value="false"/>
            <param name="full_species_name" value="false"/>
            <param name="result_as_counts" value="false"/>
            <param name="ncbi_taxonomy_ids" value="false"/>
            <param name="full_rank_taxonomy" value="false"/>
            <param name="all_taxonomic_level" value="false"/>
            <param name="cami_format_option|cami_options" value="no"/>
            <param name="taxonomic_level_option|taxonomic_option" value="no"/>
            <param name="save_bam" value="false"/>
            <param name="save_mgc" value="true"/>

            <section name="inputs">
                <conditional name="input_type">
                    <param name="selector" value="reads"/>
                    <conditional name="reads_type">
                        <param name="selector" value="single"/>
                        <param name="unpaired_reads" ftype="fastq.gz" value="test1_single.fastq"/>
                    </conditional>
                </conditional>
                <conditional name="db">
                    <param name="db_source" value="history"/>
                    <param name="database" location="https://zenodo.org/record/7778108/files/db_mOTU_v3.1.0.tar.gz"/>
                </conditional>
            </section>
            <output name="output_motus" ftype="txt">
                <assert_contents>
                    <has_text_matching expression=".*#consensus_taxonomy.*"/>
                    <has_n_lines n="34344" delta="5"/>
                    <has_size value="2300000" delta="100000"/>
                </assert_contents>
            </output>
            <output name="output_mgc" ftype="txt">
                <assert_contents>
                    <has_text_matching expression=".*# map_tax*"/>
                    <has_n_lines n="82" delta="5"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
What it does
============

The mOTUs profiler is a tool designed for taxonomic profiling of metagenomic and metatranscriptomic data.
It allows for the identification and quantification of microbial community composition directly from sequencing reads. 
mOTUs utilizes a database of marker genes identified across a wide range of microbial taxa, enabling the detection of known and unknown microorganisms in your sample data.

Additional Resources
====================

For a more comprehensive understanding of mOTUs and detailed usage instructions, please visit the mOTUs GitHub repository:

mOTUs GitHub Repository: [https://github.com/motu-tool/mOTUs]

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