annotate MT_for_MQ.xml @ 2:e7941ee539f7 draft default tip

planemo upload

<tool id="mt_for_mq" name="MT_for_MQ" version="1.0">
    <description>Tool to prepare outputs from ASaiM for Metaquantome</description>
    <requirements>
        <requirement type="package" version="1.2.1">r-tidyverse</requirement>
        <requirement type="package" version="1.3.1">r-readr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

#if $options.mode == "f" or $options.mode == "ft":
    Rscript '$__tool_directory__/MT_for_iMQ.R' '$options.input_files' '$options.mode' $options.ontology $mq_output
#elif $options.mode == "t":
    mkdir in_dir
    #for $input in $options.input_files:
        && cp '$input' 'in_dir/${input.name.rsplit('.',1)[0]}'
    #end for
    && Rscript '$__tool_directory__/MT_for_iMQ.R' in_dir t NA $mq_output
#end if

    ]]>
    </command>
    
    <inputs>
        <conditional name="options">
            <param type="select" display="radio" name="mode" label="Mode">
                <option value="f">Functional</option>
                <option value="t" selected="true">Taxonomic</option>
                <option value="ft">Functional-Taxonomic</option>
            </param>
            <when value="t">
                <param name="ontology" type="hidden" value="NA" />
                <param type="data" name="input_files" format="tsv,tabular,txt" label="Files from ASaiM for all samples (named after sample)" multiple="true" />
            </when>
            <when value="f">
                <param type="select" name="ontology" label="GO namespace" multiple="true" optional="false">
                    <option value="molecular_function">molecular function</option>
                    <option value="biological_process">biological proces</option>
                    <option value="cellular_component">cellular component</option>
                </param>
                <param type="data" name="input_files" format="tsv,tabular,txt" label="File from HIUMAnN2 renormalize function" />
            </when>
            <when value="ft">
                <param type="select" name="ontology" label="GO namespace" multiple="true" optional="false">
                    <option value="molecular_function">molecular function</option>
                    <option value="biological_process">biological proces</option>
                    <option value="cellular_component">cellular component</option>
                </param>
                <param type="data" name="input_files" format="tsv,tabular,txt" label="File from HIUMAnN2 renormalize function" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data name="mq_output" format="tabular" label="mq_${options.mode}_input.tabular"/>
    </outputs>
    
    
    <tests>
        <test>
            <param name="input_files" value="T4A.tsv,T4B.tsv,T4C.tsv,T7A.tsv,T7B.tsv,T7C.tsv" ftype="tsv"/>
            <param name="mode" value="f"/>
            <param name="ontology" value="molecular_function,biological_process"/>
            <output name="mq_output" file="mq_input.tabular">
                <assert_contents>
                    <has_text text="namespace"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    
    
    
    <help><![CDATA[

**MT2MQ**: Metatranscriptomics to Metaquantome

MT2MQ is a tool to prepare metatrascriptomic results for further analysis with MetaQuantome, which currently only supports metaproteomic data.
This tool takes in tabular files with taxonomic or functional results acquired from metatranscriptomic data. If taxonomic, the data should be the genus-level MetaPhlan results. If functional, the data should be the gene families output from HUMAnN2. Each sample and replicate should be contained in a single file, which must be named as the sample is.

**Outputs**:

MT2MQ produces a single tabular output, formatted to be used as input for Metaquantome.

    ]]></help>
    
    <citations>
        <citation type="bibtex">
            @misc{MT_for_MQ, 
            author={Crane, Marie},
            year={2020},
            title={ASaiM to MetaQuantome}
            }
        </citation>
    </citations>
</tool>