comparison metaphlan2.xml @ 1:9be4beda6482 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 40926b77d62858edbca5b04f73bb0f2aad4da31e"

0:8c82c4d90cc6

<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.0">

    <description>to profile the composition of microbial communities</description>

    <macros>
        <import>metaphlan2_macros.xml</import>

    <expand macro="requirements">
        <requirement type="package" version="2.3.0">bowtie2</requirement>
        <requirement type="package" version="2.7.10">python</requirement>
    </expand>
    
    <expand macro="stdio"/>

    <version_command>
<![CDATA[
metaphlan2.py -v
]]>
    </version_command>

    <command>
<![CDATA[
        #if $db.db_selector == "history"
            mkdir ref_db
            &&
            bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
            &&
            python '$__tool_directory__/transform_json_to_pkl.py'
                --json_input '$db.mpa_pkl'
                --pkl_output 'ref_db/metadata.pkl'
            &&
        #end if

        metaphlan2.py
            '$input_file'
            -o '$output_file'
            --input_type '${input_file.datatype.file_ext}'
            --bowtie2_exe `which bowtie2`

            #if $db.db_selector == "cached"
                #set $path = $db.cached_db.fields.path
                #set $value = $db.cached_db.fields.value
                --bowtie2db $path/$value
                --mpa_pkl $path/$value'.pkl'
            #else
                --bowtie2db 'ref_db/ref_db'
                --mpa_pkl 'ref_db/metadata.pkl'
            #end if

            --no_map

            -t '$analysis_type.analysis_type_select'
            #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
                --tax_lev '$analysis_type.tax_lev'
            #else if $analysis_type.analysis_type_select == "marker_ab_table"
                --nreads '$analysis_type.nreads'
            #else if $analysis_type.analysis_type_select == "marker_pres_table"
                --pres_th '$analysis_type.pres_th'
            #end if

            --min_cu_len '$min_cu_len'
            --min_alignment_len '$min_alignment_len'

            $ignore_viruses
            $ignore_eukaryotes
            $ignore_bacteria
            $ignore_archaea

            --stat_q '$stat_q'
            -s '$sam_output_file'
            --biom '$biom_output_file'
]]>
    </command>

    <inputs>
        <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
        <conditional name="db">
            <param name="db_selector" type="select" label="Database with clade-specific marker genes">

        <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
        <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
    </inputs>

    <outputs>
        <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
        <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: SAM file" />
        <data format="biom" name="biom_output_file" label="${tool.name} on ${on_string}: BIOM file" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="input_sequences.fasta"/>

1:9be4beda6482

<tool id="metaphlan2" name="MetaPhlAn2" version="@WRAPPER_VERSION@.1">

    <description>to profile the composition of microbial communities</description>

    <macros>
        <import>metaphlan2_macros.xml</import>

    <expand macro="requirements">
        <requirement type="package" version="2.3.0">bowtie2</requirement>
        <requirement type="package" version="2.7.10">python</requirement>
    </expand>

    <expand macro="stdio"/>

    <version_command>metaphlan2.py -v</version_command>

    <command><![CDATA[
#if $db.db_selector == "history"
    mkdir ref_db
    &&
    bowtie2-build '$db.bowtie2db' 'ref_db/ref_db'
    &&
    python '$__tool_directory__/transform_json_to_pkl.py'
        --json_input '$db.mpa_pkl'
        --pkl_output 'ref_db/metadata.pkl'
    &&
#end if

#if $input_file.datatype.file_ext.startswith("fastq")
    #set ext='fastq'
#else
    #set ext=$input_file.datatype.file_ext
#end if

metaphlan2.py
    '$input_file'
    -o '$output_file'
    --input_type $ext
    --bowtie2_exe `which bowtie2`

    #if $db.db_selector == "cached"
        #set $path = $db.cached_db.fields.path
        #set $value = $db.cached_db.fields.value
        --bowtie2db $path/$value
        --mpa_pkl $path/$value'.pkl'
    #else
        --bowtie2db 'ref_db/ref_db'
        --mpa_pkl 'ref_db/metadata.pkl'
    #end if

    --no_map

    -t '$analysis_type.analysis_type_select'
    #if $analysis_type.analysis_type_select == "rel_ab" or $analysis_type.analysis_type_select == "rel_ab_w_read_stats"
        --tax_lev '$analysis_type.tax_lev'
    #else if $analysis_type.analysis_type_select == "marker_ab_table"
        --nreads '$analysis_type.nreads'
    #else if $analysis_type.analysis_type_select == "marker_pres_table"
        --pres_th '$analysis_type.pres_th'
    #end if

    --min_cu_len '$min_cu_len'
    --min_alignment_len '$min_alignment_len'

    $ignore_viruses
    $ignore_eukaryotes
    $ignore_bacteria
    $ignore_archaea

    --stat_q '$stat_q'
    -s '$sam_output_file'
    --biom '$biom_output_file'
    ]]></command>

    <inputs>
        <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file"/>
        <conditional name="db">
            <param name="db_selector" type="select" label="Database with clade-specific marker genes">

        <param argument="--ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?"/>
        <param argument="--stat_q" type="float" value="0.1" label="Quantile value for the robust average"/>
    </inputs>

    <outputs>
        <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Community profile" />
        <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file" />
        <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="input_sequences.fasta"/>