comparison multigps.xml @ 17:3ea58bab5819 draft

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16:786468a702b0

    <requirements>
        <requirement type="package" version="0.74">multigps</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            #set output_dir = $output_html.files_path
            mkdir -p $output_dir &&
            multigps
            ## General options
            --design '$design_file'

            && mv $output_dir/*.html '$output_html'
            && mv $output_dir/*.table.txt '$all_events_table'
        ]]>
    </command>
    <configfiles>
        <configfile name="design_file">
<![CDATA[
#for $cond_i, $condition_items in enumerate($condition_repeat):
    #for $signal_items in $condition_items['signal_repeat']:
        #set signal = $signal_items['signal']
        #set replicate_name = $signal_items['replicate_name']

                        </param>
                    </when>
                </conditional>
                <!-- Scaling data -->
                <conditional name="scale_data_cond">
                    <param  name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method described by Liang &amp; Ketes, BMC Bioinformatics 2012.">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="yes">
                        <param  name="scaling" type="select" label="Use signal vs control scaling?">

 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.

    </help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
    </citations>
</tool>

17:3ea58bab5819

    <requirements>
        <requirement type="package" version="0.74">multigps</requirement>
    </requirements>
    <command detect_errors="aggressive">
        <![CDATA[
            #set design_file = '$build_design_file'
            #set output_dir = $output_html.files_path
            mkdir -p $output_dir &&
            multigps
            ## General options
            --design '$design_file'

            && mv $output_dir/*.html '$output_html'
            && mv $output_dir/*.table.txt '$all_events_table'
        ]]>
    </command>
    <configfiles>
        <configfile name="build_design_file">
<![CDATA[
#for $cond_i, $condition_items in enumerate($condition_repeat):
    #for $signal_items in $condition_items['signal_repeat']:
        #set signal = $signal_items['signal']
        #set replicate_name = $signal_items['replicate_name']

                        </param>
                    </when>
                </conditional>
                <!-- Scaling data -->
                <conditional name="scale_data_cond">
                    <param  name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method.[2]">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="yes">
                        <param  name="scaling" type="select" label="Use signal vs control scaling?">

 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.

    </help>
    <citations>
        <citation type="bibtex">
            @article{Mahony2014,
            journal = {PLOS Computational Biology},
            author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
            title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
            year = {2014},}
            volume = {10},
            number = {3},
            pages = {e1003501},}
        </citation>
        <citation type="bibtex">
            @article{Liang2012,
            journal = {BMC Bioinformatics},
            author = {2. Liang, Ketes},
            title = {Normalization of ChIP-seq data with control},
            year = {2012},}
        </citation>
    </citations>
</tool>