annotate motus_merge.xml @ 0:d20f3b9a59a2 draft default tip

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

<tool id="mereg_mOTUs_tables" name="Merge" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>Merge mOTUs aboundance or count tables</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 merge
        -db '$DATABASE_DIR'
        -i '${','.join([str($file) for $file in $files])}'
        #if $add_profiles
        -a '$add_profiles'
        #end if
        #if $biom_format
        -o '$output_biom'
        $biom_format
        #else
        -o '$output_txt'
        #end if
    ]]></command>
    <inputs>
        <param name="files" type="data" format="txt" multiple="true" label="mOTU profiles to merge"/>
        <param argument="add_profiles" type="text" label="Add pre-computed profiles" help="Add pre-computed profiles from different environmental samples" optional="true"/>
        <param argument="biom_format" type="boolean" truevalue="-B" falsevalue="" checked="false" label="Output in BIOM format?"/>
        <conditional name="db">
            <param name="db_source" type="select" label="mOTUs Database">
                <option value="cached">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>
    </inputs>
    <outputs>
        <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: Merged taxon tables">
            <filter>not biom_format</filter>
        </data>
        <data name="output_biom" format="biom1" label="${tool.name} on ${on_string}: BIOM Output">
            <filter>biom_format</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="files" value="SAMEA2466887-default.motus,SAMEA2466889-default.motus"/>
            <param name="biom_format" value="false"/>
            <conditional name="db">
                <!-- Local db -->
                <param name="db_source" value="history"/>
                <param name="database" location="https://zenodo.org/record/7778108/files/db_mOTU_v3.1.0.tar.gz"/>
                <!-- <param name="database" value="db_mOTU_v3.1.0.tar.gz"/> -->
            </conditional>
            <output name="output_txt" ftype="txt">
                <assert_contents>
                    <has_text_matching expression="Enterobacterales sp.*"/>
                    <has_text_matching expression="Klebsiella michiganensis.*"/>
                    <has_text_matching expression="Streptococcus sp.*"/>
                    <has_text_matching expression="Streptococcus pseudopneumoniae.*"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        
What it does
============

The mOTUs tool performs taxonomic profiling of metagenomics and metatrancriptomics samples.

mOTUs merge is specifically developed for merging and consolidating taxonomic profiles generated by the mOTU profiler. 
It facilitates the combination of taxon abundance or count data from multiple samples or datasets into a single output.

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