TEdiff.xml

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<tool id="TEdiff" name="TEdiff" version="1.0.0" hidden="false">
    <description>Differential expression analysis of transposable elements</description>
    <version_command interpreter="Rscript">TEdiff.R --version=TRUE</version_command>
    <command interpreter="Rscript">TEdiff.R --args --FDR_level=$FDR_level --count_column=$count_column --count_file=\"$count_file\" experiment_formula=\"$experiment_formula\" --sample_names=\"$sample_names\" --outdir=\"$htmlfile.files_path\" --htmlfile=\"$htmlfile\" 2> \dev\null
    </command>

    <inputs>
        <param name="count_file" type="data" format="tabular" label="count file computed with TEcount" />
        <param name="count_column" type="integer" value="2" label="number of the first column with read counts (ex: 2 if the rosette file as only one variable)"/>
        <param name="sample_names" area="True" size="5x180" type="text" value="sample_name_1:replicat_1,sample_name_1:replicat_2,...,sample_name_n:replicat_1,sample_name_n:replicat_2" label="comma separated list of names of the different samples in the same order as in the count file (example for n samples with 2 replicats:
            sample_name_1:replicat_1,sample_name_1:replicat_2,...,sample_name_n:replicat_1,sample_name_n:replicat_2)"/>
        <param name="experiment_formula" area="True" size="1x180" type="text" value="sample_name:replicat" label="formula corresponding to the names (example: sample_name:replicat:condition)"/>
        <param name="FDR_level" type="float" value="0.05" min="0.0" max="1.0" label="FDR threshold for the analysis"/>
    </inputs>

    <outputs>
        <data format="html" name="htmlfile" label="TEdiff_results.html" />
    </outputs>

    <requirements>
        <requirement type="package">Rscript</requirement>
    </requirements>

    <help>
TEdiff documentation:
======================
The program performs differential expression analysis using the program DESeq2 and the count table generated by TEcount.
This tool produces an HTML output with clickable images, allowing to download the PDF files.
    </help>
</tool>