annotate matCorAddVar.xml @ 0:d0b77b926863 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"

<tool id="matCorAddVar" name="matCorAddVar" version="1.0" profile="16.04" workflow_compatible="true">

    <description>determine the correlation circles that can be overlaid and compute the correlations</description>

    <requirements>
        <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda -->
        <requirement type="package" version="2.0">r-argparse</requirement>
        <!-- <requirement type="package" version="0.3">viscorvar</requirement> -->
    </requirements>

    <stdio>
        <!-- <exit_code range="1:" level="fatal" /> -->
    </stdio>
 
    <command detect_errors="aggressive">
        <![CDATA[
        Rscript
        ${__tool_directory__}/matCorAddVar_wrapper.R
        --input_rdata ${input_rdata}
        ##--cutoff_comp ${cutoff_comp}
        --cutoff_comp 0.775
        #if str($var_of_interest_file) !='':
            --interest_var_file ${var_of_interest_file}
        #end if
        --block_Y_file ${block_Y}
        --output_rdata ${output_rdata}
        --output_response_var ${output_response_var}
        --output_blocks_comb ${output_blocks_comb}
        ]]>
    </command>

    <inputs>
        <param name="input_rdata" type="data" format="rdata"
               label="Input RData file from block.SPLSDA"
               help="This is the RData output file from the block.splsda function." />
        <param name="block_Y" type="data" format="tabular"
               label="Block Y"
               help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
        <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
        <param name="var_of_interest_file" type="data" format="txt" optional="true"
               label="Variables of interest (Optional)"
               help="these variables have to belong to datasets that can be superimposed"/>
<!--         <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
               label="Cutoff comp"
               help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
    </inputs>

    <outputs>
        <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" />
        <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
        <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
    </outputs>

    <tests>
    </tests>

    <help>
    </help>

</tool>