comparison rmarkdown_deseq2_count_matrix.xml @ 1:629323b5fc0c draft

update tool

0:c1f718dd6c7a

    </stdio>
    <command><![CDATA[
Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
                        -e $echo
                        -c $count_data
                        -C $col_data
                        -D '$design_formula'
                        -k $contrast_condition
                        -T $treatment
                        -k $control
                        -r $report
                        -d $report.files_path
                        -s $sink_message
                        -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
                    ]]></command>
    <inputs>
        <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
               truevalue="TRUE" falsevalue="FALSE"/>
        <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
        <param type="data" name="col_data" label="column data" optional="False" format="txt,csv" multiple="False"/>
        <param type="text" name="design_formula" label="design formula"
               help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10;                     is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
               optional="False" value="~ condition_1 + condition_2"/>
        <param type="text" name="contrast_condition" label="condition"
               help="A condition name specified in the design formula" optional="False" value="condition_1"/>
        <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
               optional="False"/>
        <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
               optional="False"/>
    </inputs>
    <outputs>
        <data name="report" format="html" label="DESeq2 report" hidden="false"/>
        <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
              hidden="false"/>
        <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
              hidden="false"/>
    </outputs>
    <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>

1:629323b5fc0c

    </stdio>
    <command><![CDATA[
Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
                        -e $echo
                        -c $count_data
                        -n '$count_matrix_column_names'
                        -C $col_data
                        -D '$design_formula'
                        -k $contrast_condition
                        -T $treatment
                        -K $control
                        -r $report
                        -d $report.files_path
                        -s $sink_message
                        -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
                    ]]></command>
    <inputs>
        <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
               truevalue="TRUE" falsevalue="FALSE"/>
        <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
        <param type="text" name="count_matrix_column_names" label="column names"
               help="This field is used to update the column names of count data matrix. Column names are separated by comma (,). For example, 'column_1, column_2, column_3, column_4'"
               optional="True" area="True" size="5x25"></param>
        <param type="data" name="col_data" label="column data (from file)" optional="False" format="txt,csv" multiple="False"/>
        <param type="text" name="design_formula" label="design formula"
               help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10;                     is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
               optional="False" value="~ condition_1 + condition_2">
            <sanitizer>
                <valid>
                    <add value="~"/>
                </valid>
            </sanitizer>
        </param>
        <param type="text" name="contrast_condition" label="condition"
               help="A condition name specified in the design formula" optional="False" value="condition_1"/>
        <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
               optional="False" value="treated"/>
        <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
               optional="False" value="untreated"/>
    </inputs>
    <outputs>
        <data name="report" format="html" label="DESeq2 report" hidden="false"/>
        <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
              hidden="false"/>
        <data name="deseq2" format="rdata" label="DESeq2 R objects" from_work_dir="deseq2.RData"
              hidden="false"/>
        <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
              hidden="false"/>
    </outputs>
    <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>