annotate taxonkit_profile2cami.xml @ 4:d38b9fdf04e0 draft default tip

planemo upload for repository https://github.com/shenwei356/taxonkit commit 491bc028e8546bee626ab6f6168a706ab2f5324a

<tool id="profile2cami" name="Profile2CAMI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Convert metagenomic profile table to CAMI format</description>
    <macros>
        <import>macros.xml</import>
    </macros>    
    <expand macro="biotools"/>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        taxonkit profile2cami
        --data-dir '${taxonomy.fields.path}'
        --abundance-field '${abundance_field}'
        --taxid-field '${taxid_field}'

        $percentage
        $recompute_abd
        $keep_zero
        $no_sum_up

        #if $sample_id:
            -s '${sample_id}'
        #end if
        #if $taxonomy_id:
            -t '${taxonomy_id}'
        #end if
        #if $ranks:
            --show-rank '${ranks}'
        #end if
        ${input_file}
        > '${cami_output}'
    ]]>
    </command>
    <inputs>
        <param name="input_file" type="data" format="txt" label="Input Profile File" help="A tab-delimited profile file with TaxId and abundance columns." />
        <param argument="--taxonomy" type="select" label="NCBI taxonomy" help="This NCBI database is used to map human-readable taxon names to TaxId's.">
            <options from_data_table="ncbi_taxonomy">
                <validator message="No NCBI database is available" type="no_options"/>
            </options>
        </param>
        <param name="abundance_field" type="integer" value="2" label="Abundance Field Index" help="Field index of abundance in the input data." />
        <param name="taxid_field" type="integer" value="1" label="TaxId Field Index" help="Field index of TaxId in the input data." />
        <param name="percentage" type="boolean" value="false" label="Abundance in Percentage" help="Check if the abundance values are in percentage." truevalue="-p" falsevalue=""/>
        <param name="recompute_abd" type="boolean" value="false" label="Recompute Abundance" help="Check to recompute abundance if some TaxIds are deleted in the current taxonomy version." truevalue="-R" falsevalue=""/>
        <param name="keep_zero" type="boolean" value="false" label="Keep Zero Abundances" help="Check to keep taxons with abundance of zero." truevalue="-0" falsevalue=""/>
        <param name="no_sum_up" type="boolean" value="false" label="Do Not Sum Up Abundance" help="Do not sum up abundance from child to parent TaxIds." truevalue="-S" falsevalue="" />
        <param name="sample_id" type="text" value="" label="Sample ID" help="Optional sample ID to include in the result file." />
        <param name="taxonomy_id" type="text" value="" label="Taxonomy ID" help="Optional taxonomy ID to include in the result file." />
        <param name ="ranks" argument="--show-rank" type="select" multiple="true" label="Show Ranks" help="Specify the ranks to show in the result file (default [superkingdom,phylum,class,order,family,genus,species,strain]).">
            <option value="superkingdom">Superkingdom</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="species">Species</option>
            <option value="strain">Strain</option>
        </param>
    </inputs>
    <outputs>
        <data name="cami_output" format="tsv" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- Test 1: Basic functionality with default parameters -->
        <test expect_num_outputs="1">
            <param name="input_file" value="abundance.tsv" ftype="tsv" />
            <output name="cami_output" file="output1_basic_functionality.tsv" />
        </test>

        <!-- Test 2: Using percentage flag -->
        <test expect_num_outputs="1">
            <param name="input_file" value="abundance.tsv" ftype="tsv" />
            <param name="percentage" value="true" />
            <output name="cami_output" file="output2_percentage_flag.tsv" />
        </test>

        <!-- Test 3: Recomputing abundance with deleted TaxIds -->
        <test expect_num_outputs="1">
            <param name="input_file" value="abundance.tsv" ftype="tsv" />
            <param name="recompute_abd" value="true" />
            <output name="cami_output" file="output3_recompute_abd.tsv" />
        </test>

        <!-- Test 4: Profile2Cami with all parameters checked -->
        <test expect_num_outputs="1">
            <param name="input_file" value="abundance.tsv" ftype="tsv" />
            <param name="percentage" value="true" />
            <param name="recompute_abd" value="true" />
            <param name="keep_zero" value="true" />
            <param name="no_sum_up" value="true" />
            <output name="cami_output" file="output4_all_param.tsv" />
        </test>
        </tests>
        <help>
        <![CDATA[
            **What is Profile2CAMI**

            Profile2CAMI is a tool for converting metagenomic profile tables to CAMI format.

            **Inputs**

            - A tab-delimited profile file with TaxId and abundance columns.

            **Outputs**

            - A CAMI formatted file.

            For more information, please refer to the tool's documentation.
        ]]>
        </help>
    <expand macro="citations" />
</tool>