comparison metaphlan2.xml @ 2:f60773e921fa draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit bfc25b2695b9689c60101f84162610194a33c886"

1:9be4beda6482

#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"

    -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">
                <option value="cached" selected="true">Locally cached</option>
                <option value="history">From history</option>
            </param>

        <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"/>
            <param name="db_selector" value="history" />
            <param name="mpa_pkl" value="marker_metadata.json" />
            <param name="bowtie2db" value="marker_sequences.fasta" />
            <param name="analysis_type_select" value="rel_ab" />
            <param name="taxonomic_level" value="a" />
            <param name="min_cu_len" value="2000" />
            <param name="min_alignment_len" value="0" />
            <param name="ignore_viruses" value="" />
            <param name="ignore_eukaryotes" value="" />
            <param name="ignore_bacteria" value="" />
            <param name="ignore_archaea" value="" />
            <param name="stat_q" value="0.1" />
            <output name="output_file" file="community_profile.tabular"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

2:f60773e921fa

#else
    #set ext=$input_file.datatype.file_ext
#end if

metaphlan2.py
    #if $input_file.datatype.file_ext.endswith(".gz")
        <(zcat '$input_file')
    #else if $input_file.datatype.file_ext.endswith(".bz2")
        <(bzcat '$input_file')
    #else
        '$input_file'
    #end if
    -o '$output_file'
    --input_type $ext
    --bowtie2_exe `which bowtie2`

    #if $db.db_selector == "cached"

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

    <inputs>
        <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2,fasta,fasta.gz,fasta.bz2,sam" label="Input file"/>
        <conditional name="db">
            <param name="db_selector" type="select" label="Database with clade-specific marker genes">
                <option value="cached" selected="true">Locally cached</option>
                <option value="history">From history</option>
            </param>

        <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" ftype="fasta"/>
            <param name="db_selector" value="history" />
            <param name="mpa_pkl" value="marker_metadata.json" />
            <param name="bowtie2db" value="marker_sequences.fasta"  ftype="fasta"/>
            <param name="analysis_type_select" value="rel_ab" />
            <param name="taxonomic_level" value="a" />
            <param name="min_cu_len" value="2000" />
            <param name="min_alignment_len" value="0" />
            <param name="ignore_viruses" value="" />
            <param name="ignore_eukaryotes" value="" />
            <param name="ignore_bacteria" value="" />
            <param name="ignore_archaea" value="" />
            <param name="stat_q" value="0.1" />
            <output name="output_file" file="community_profile.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="input_file" value="input_sequences.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="db_selector" value="history" />
            <param name="mpa_pkl" value="marker_metadata.json" />
            <param name="bowtie2db" value="marker_sequences.fasta"  ftype="fasta"/>
            <param name="analysis_type_select" value="rel_ab" />
            <param name="taxonomic_level" value="a" />
            <param name="min_cu_len" value="2000" />
            <param name="min_alignment_len" value="0" />
            <param name="ignore_viruses" value="" />
            <param name="ignore_eukaryotes" value="" />
            <param name="ignore_bacteria" value="" />
            <param name="ignore_archaea" value="" />
            <param name="stat_q" value="0.1" />
            <output name="output_file" file="community_profile.tabular" ftype="tabular"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**