Mercurial > repos > iuc > raceid_diffgene

<tool id="raceid_diffgene" name="RaceID differential gene expression analysis" version="@VERSION@.0">
    <description>Identify differentially regulated genes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    Rscript '@SCRIPT_DIR@/raceID_diffgenes.R' '@SCRIPT_DIR@' '$rconf_source'

    #if $compare_clusters_select.do_compare_clusters.value == "T":
        &&
        mkdir '${out_html.files_path}' &&
        mv plot_*.svg '${out_html.files_path}' &&

        echo '<html><head></head>
        <body>
        <h1>RaceID Differential Gene Analysis</h1>
        <br /><h3>Expression of ${compare_clusters_select.gene} between ${compare_clusters_select.cl1} and ${compare_clusters_select.cl2}</h3>
        <img src="plot_diffgenes.svg" ><br />
        </body>
        </html>' > '$out_html'
    #end if

    ]]></command>

    <configfiles>
        <configfile name="rconf_source" >
            sc = readRDS( '$inp_rdat' )

            c_pval = as.numeric( '$pval' )
            generate_extable = as.logical( '$gen_gexpr_table.value' )
            outtable_dir = 'tables'
            compare_clusters = as.logical( '$compare_clusters_select.do_compare_clusters.value' )

            #if $compare_clusters_select.do_compare_clusters.value == "T":
            gene_name = '$compare_clusters_select.gene'
            clust1 = '$compare_clusters_select.cl1'
            clust2 = '$compare_clusters_select.cl2'
            mcount = as.integer( '$compare_clusters_select.mincount' )
            #end if
        </configfile>
    </configfiles>

    <inputs>
        <param name="inp_rdat" type="data" format="rdata" label="Count matrix with clusters" help="This file is the output of the RaceID pipeline." />
        <param name="pval" type="float" value="0.01" min="1e-10" max="0.5" label="Retain genes with p-value smaller than threshold" help="The p-value for observing the difference in mean expression between the cluster and all cells based on binomial counting statistics." />
        <param name="gen_gexpr_table" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Generate table of all differentially expressed genes?" />
        <conditional name="compare_clusters_select">
            <param name="do_compare_clusters" type="select" label="Compare the expression of a specific gene between two sets of clusters?" >
                <option value="T" >Yes</option>
                <option value="F" selected="true" >No</option>
            </param>
            <when value="F" />
            <when value="T" >
                <param name="gene" type="text" label="Gene name of interest" >
                    <sanitizer invalid_char="" >
                        <valid initial="string.letters,string.digits">
                            <add value="_"/><add value="+" /><add value="-" />
                        </valid>
                    </sanitizer>
                </param>
                <param name="cl1" type="text" value="1" label="Cluster set 1" help="e.g. if you wish to compare cluster 2 to clusters 1 and 3, then type '2' here and '1,3' in the next input." >
                    <sanitizer invalid_char="" >
                        <valid initial="string.digits"><add value="," /></valid>
                    </sanitizer>
                </param>
                <param name="cl2" type="text" value="2" label="Cluster set 2" help="You can also compare sets of clusters to one another: e.g. 1,4,5 against 2,3." >
                    <sanitizer invalid_char="" >
                        <valid initial="string.digits"><add value="," /></valid>
                    </sanitizer>
                </param>
                <param name="mincount" type="integer" value="5" min="1" label="Only count genes with more than this number of transcripts in at least one cell within Cluster set 1 or Cluster set 2" />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="out_html" format="html" label="${tool.name} on ${on_string}: Web Report" />
        <data format="tsv" name="out_tables" label="${tool.name} on ${on_string}: DiffExpr Tables" >
            <discover_datasets pattern="__designation_and_ext__" directory="tables" visible="true" />
       </data>
    </outputs>

    <tests>
        <test>
            <param name="inp_rdat" value="in_diffgene.rdat" />
            <output name="out_html" value="out_diffgene1.html" />
            <!-- verify just two of the outputs -->
            <output name="out_tables" >
                <!-- Problems here... help appreciated -->
                <discovered_dataset designation="gdiff_cl.1" ftype="tsv" file="gdiff_cl.1.tsv" />
                <discovered_dataset designation="gdiff_cl.2" ftype="tsv" file="gdiff_cl.2.tsv" />
            </output>
        </test>
        <test>
            <!-- Diff Cluster plot only -->
            <param name="inp_rdat" value="in_diffgene.rdat" />
            <param name="pval" value="0.05" />
            <param name="gen_gexpr_table" value="F" />
            <param name="do_compare_clusters" value="T" />
            <param name="gene" value="1110038F14Rik__chr15" />
            <param name="cl1" value="1" />
            <param name="cl2" value="2,3" />
            <param name="mincount" value="2" />
            <output name="out_html" value="out_diffgene2.html" />
        </test>
    </tests>
    <help><![CDATA[
*****************
RaceID Diff Genes
*****************

Generates a table of all differentially expressed genes, and a plot representing the expression of a specific gene of interest between different clusters.

The RaceID pipeline must be run prior to using this tool, as the input of this tool is generated from the output of the pipeline.


    ]]></help>
    <expand macro="citations" />
</tool>