<tool id="askor_de" name="AskoR DE" version="0.2">
    <description>EdgeR for AskOmics</description>
    <requirements>
        <requirement type="package" version="3.34.6">bioconductor-limma</requirement>
        <requirement type="package" version="1.4.30">r-statmod</requirement>
        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
        <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
        <requirement type="package" version="0.7.0">r-ggrepel</requirement>
        <requirement type="package" version="3.0.1">r-gplots</requirement>
        <requirement type="package" version="1.4.4">r-optparse</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      export ASKOR_PATH='$__tool_directory__'

      &&

      Rscript '$__tool_directory__/AskoR_DE.R'
          --out '${out_pdf}'
          --outdir askor_output
          --fileofcount '${fileofcounts}'
          --sample '${samples}'
          --contrasts '${contrasts}'
          #if $adv.organism
            --org '${adv.organism}'
          #end if
          #if $adv.colgenes
            --col_genes ${adv.colgenes}
          #end if
          #if $adv.palette
            --palette '${adv.palette}'
          #end if
          #if $selection.sel
            --select '${selection.sel}'
          #end if
          #if $selection.remove
            --remove '${selection.remove}'
          #end if
          #if $thresholds.th_cpm
            --th_cpm ${thresholds.th_cpm}
          #end if
          #if $thresholds.rep
            --rep ${thresholds.rep}
          #end if
          #if $thresholds.th_FDR
            --th_FDR ${thresholds.th_FDR}
          #end if
          #if $stats.norm
            --normalization '${stats.norm}'
          #end if
          #if $stats.adj
            --adj '${stats.adj}'
          #end if
          #if $stats.glm
            --glm '${stats.glm}'
          #end if
          #if $adv.nh
            --nh ${adv.nh}
          #end if
    ]]></command>
    <inputs>
        <param format="tabular,csv" name="fileofcounts" type="data" label="File of counts" />
        <param format="tabular,tsv" name="samples" type="data" label="Descriptions of the samples" />
        <param format="tabular,tsv" name="contrasts" type="data" label="Descriptions of the contrasts" />
        <section name="adv" title="Format options" expanded="false">
            <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" />
            <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /-->
            <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" />
            <param name="organism" type="text" label="Organism" value="Asko" optional="true" />
            <param name="nh" type="integer" label="Number of genes in the heatmap" value="50" optional="true" />
        </section>
        <section name="selection" title="Samples selection options" expanded="false">
            <param name="sel" type="text" label="List of selected samples (separated by comma)" optional="true" />
            <param name="remove" type="text" label="List of removed samples (separated by comma)" optional="true" />
        </section>
        <section name="thresholds" title="Threshold options" expanded="false">
            <param name="th_cpm" type="float" label="Minimum CPM value for selecting a gene" value="0.5" optional="true" />
            <param name="rep" type="integer" label="Number of samples with CPM > th_comp for selecting a gene" value="3" optional="true" />
            <param name="th_FDR" type="float" label="FDR threshold for reporting a differential gene" value="0.05" optional="true" />
        </section>
        <section name="stats" title="Statistics options" expanded="false">
            <param name="norm" type="select" label="Normalization method">
                <option value="TMM">TMM</option>
                <option value="RLE">RLE</option>
                <option value="upperquartile">Upperquartile</option>
                <option value="none">None</option>
            </param>
            <param name="glm" type="select" label="GLM method">
                <option value="qlf">qlf</option>
                <option value="lrt">lrt</option>
            </param>
            <param name="adj" type="select" label="Multitest correction method">
                <option value="fdr">fdr</option>
                <option value="holm">holm</option>
                <option value="hochberg">hochberg</option>
                <option value="hommel">hommel</option>
                <option value="bonferroni">bonferroni</option>
                <option value="BH">BH</option>
                <option value="BY">BY</option>
                <option value="none">none</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" />
        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="tabular" visible="true" directory="askor_output" />
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fileofcounts" ftype="csv" value="counts.csv" />
            <param name="samples" ftype="tabular" value="Samples.txt" />
            <param name="contrasts" ftype="tabular" value="Contrasts.txt" />
            <section name="adv">
                <param name="colgenes" value="3" />
            </section>
            <section name="thresholds">
                <param name="th_cpm" value="10" />
            </section>
            <output name="out_pdf" file="out.pdf" compare="sim_size"/>
            <output name="output">
                <discovered_dataset designation="AskoAvsK" ftype="tabular" file="AskoAvsK.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1AvsT1K" ftype="tabular" file="AskoT1AvsT1K.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1vsT0" ftype="tabular" file="AskoT1vsT0.txt" compare="sim_size" />
                <discovered_dataset designation="AskoT1vsT2" ftype="tabular" file="AskoT1vsT2.txt" compare="sim_size" />
                <discovered_dataset designation="condition.asko" ftype="tabular" file="condition.asko.txt" compare="sim_size" />
                <discovered_dataset designation="context.asko" ftype="tabular" file="context.asko.txt" compare="sim_size" />
                <discovered_dataset designation="contrast.asko" ftype="tabular" file="contrast.asko.txt" compare="sim_size" />
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/).

Example tabular input file of counts:

============ ========== =============== =========== =========== ======
miRNA	     read_count	precursor	    total	    A32	        A34
------------ ---------- --------------- ----------- ----------- ------
GL349623_679 346.00     GL349623_679    146.00      16.00       130.0
GL349624_956 13.00      GL349624_956    13.00       0           13.0
============ ========== =============== =========== =========== ======

Example tabular sample description file:

============ ========== =============== ===========
ID           condition  stage           treatment
------------ ---------- --------------- -----------
A32          T3A        T3              Acetone
A34          T3A        T3              Acetone
============ ========== =============== ===========

Example tabular contrast description file:

============ ========================= =======================
Contrast     context1_of@Context       context2_of@Context
------------ ------------------------- -----------------------
T1vsT0       T1                        T0
T1vsT2       T1                        T2
============ ========================= =======================
    ]]></help>
    <citations>
    </citations>
</tool>