comparison multigps.xml @ 47:7c3ef587aed9 draft

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46:9eb54f2ef321

            --expt '$expt'
            --format $expt.ext
            #if str($ctrl) != 'None':
                --ctrl '$ctrl'
            #end if
            #if str($verbose) == 'yes':
                --verbose
            #end if
            --threads=\${GALAXY_SLOTS:-4}
            --geninfo '$chromInfo'
            ############################
            ## Advanced options
            ############################

    <inputs>
        <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
            <validator type="unspecified_build" />
        </param>
        <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
        <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        <!--
        ############################
        ## Advanced options
        ############################
        -->

                    </when>
                </conditional>
            </when>
            <when value="hide" />
        </conditional>
        <!--
        <param name="output_process_log" type="select" label="Output MultiGPS process log?">
            <option value="no" selected="True">No</option>
            <option value="yes">Yes</option>
        </param>
        -->
    </inputs>
    <outputs>
        <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
        <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/>
        <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
            <param name="verbose" value="no" />
            <param name="advanced_options_cond" value="hide" />
            <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
            <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
            <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="sacCer3" />
            <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="sacCer3" />
            <param name="verbose" value="no" />
            <param name="advanced_options_cond" value="display" />
            <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
            <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
            <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
        </test>

 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.

* **Running MultiGPS:**

 - **binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
 - **Perform binding model updates?** - Perform binding model updates?
 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
 - **Spline smoothing parameter** - Smoothing parameter for smoothing cubic spline.

47:7c3ef587aed9

            --expt '$expt'
            --format $expt.ext
            #if str($ctrl) != 'None':
                --ctrl '$ctrl'
            #end if
            --threads=\${GALAXY_SLOTS:-4}
            --geninfo '$chromInfo'
            ############################
            ## Advanced options
            ############################

    <inputs>
        <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
            <validator type="unspecified_build" />
        </param>
        <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
        <!--
        ############################
        ## Advanced options
        ############################
        -->

                    </when>
                </conditional>
            </when>
            <when value="hide" />
        </conditional>
    </inputs>
    <outputs>
        <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/>
        <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/>
        <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
            <param name="advanced_options_cond" value="hide" />
            <output name="output_html" file="hg19_output_html1.html" ftype="html" lines_diff="12"/>
            <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
            <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
        </test>
        <test>
            <param name="expt" value="expt_hg19.scidx" ftype="bam" dbkey="hg19" />
            <param name="ctrl" value="cntrl_hg19.scidx" ftype="bam" dbkey="hg19" />
            <param name="advanced_options_cond" value="display" />
            <output name="output_html" file="hg19_output_html2.html" ftype="html" lines_diff="12"/>
            <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
            <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
        </test>

 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.

* **Running MultiGPS:**

 - **Optional binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
 - **Perform binding model updates?** - Perform binding model updates?
 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
 - **Spline smoothing parameter** - Smoothing parameter for smoothing cubic spline.