annotate lfq_protein_quant.xml @ 0:bb199421f731 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant commit 26ff08776f90f96646598a19cfcf57d42aa4a43b

<tool id="lfq_protein_quant" name="Label free protein" version="1.0">
    <description>
        summarisation and quantitation
    </description>
    <requirements>
        <requirement type="package" version="2.2.0">bioconductor-msnbase</requirement>
        <requirement type="package" version="2.12.0">bioconductor-mzr</requirement>
        <requirement type="package" version="1.2.1">r-tidyverse</requirement>
        <requirement type="package" version="1.1_18_1">r-lme4</requirement>
        <requirement type="package" version="0.1.0">r-furrr</requirement>
        <requirement type="package" version="0.7.5">r-msqrob</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
        ln -s '${moff_file}' moff.tsv &&
        ln -s '${meta_file}' meta.tsv &&
        Rscript '$__tool_directory__/quantitation.r'
            moff.tsv
            meta.tsv
            $only_summarisation
            \${GALAXY_SLOTS:-4}
    ]]>
    </command>
    <inputs>
        <param name="moff_file" type="data" format="tabular"
               label="Peptide summary output from moFF or other peptide quantitation tools" />
        <param name="meta_file" type="data" format="tabular" label="Metadata with sample names and condition" />
        <param name="only_summarisation" type="boolean" truevalue="1" falsevalue="0"
            label="Only summarisiation" help="This option will deactivate the quantifiation of data." />

    </inputs>
    <outputs>
        <data format="tabular" name="quant" from_work_dir="quantitation.tsv" label="${tool.name} on ${on_string}: quantification">
            <filter>not only_summarisation</filter>
        </data>
        <data format="tabular" name="summary" from_work_dir="summarised_proteins.tsv" label="${tool.name} on ${on_string}: summary"/>
    </outputs>
    <tests>
        <test>
            <param name="moff_file" value="moff.tab"/>
            <param name="meta_file" value="meta.tab"/>
            <param name="only_summerisation" value="true"/>
            <output name="quant" file="quantitation.tsv" />
            <output name="summary" file="summarised_proteins.tsv" />
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

Protein summarisation and label free quantitation.

----

    **Inputs** 

    - Quantification input: Tabular file with the summary output from moFF or in case other tools were used for peptide quantitation with the following columns: 'peptides' containing the amino acid sequence; 'prot' with the Uniprot Accession and then one column per sample with the quantitation values.

            ::

                  peptides     prot       sample1    sample2
                  AAABDEK      B9DM54     1809446    563862
                  TELATASDR    Q9CFE8     294282     457023
                  AMGLATK      P85660     194023     428277
                    ...
                    ...


    - Metadata input: Separate columns with sample names, condition and optionally also lab and machine. Sample names must match exactly the sample names from the peptide quantitation columns in the previous tabular file.


            ::

                  sample     condition 
                  sample1    healthy
                  sample2    disease
                    ...
                    ...


    **Options** 

    - Summarisation only: Summarisation is done through robust regression to take also the peptide effect into account. In case only sample column is provided median protein intensity is calculated.
    - Summarisation and quantification: Relative quantification is performed according to the information provided in the metadata file. 


    **Outputs** 

    - Summarised protein output: Uniprot accession and quantitation values per sample and protein
    - Quantification output: Uniprot accession, comparison between conditions, fold change, p-value, q-value

        ]]>
    </help>
    <citations>
        <citation type="doi">10.1074/mcp.M115.055897</citation>
        <citation type="doi">10.1093/bioinformatics/btr645</citation>
    </citations>
</tool>