comparison hicCorrelate.xml @ 7:602a0c6f4bb0 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457

6:8187f841afea

            #if $method and $method is not None:
                --method $method
            #end if
            $log1p

            #if $use_range.select_use_range == "yes_use_range":
                --range $range_min:$range_max
            #end if

            #if $chromosomes:
                --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
            #end if
            
            --colorMap $colormap

            --outFileNameHeatmap ./heatmap.png
            --outFileNameScatter ./scatter.png
]]>
    </command>

            <option value="spearman">Spearman</option>
            <option selected="true" value="pearson">Pearson</option>
        </param>
        <param name="log1p" type="boolean" argument="--log1p"  truevalue="--log1p" falsevalue=""
            label="Use the log1p of the matrix values" help="(--log1p)" />
        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
                <option value="no_use_range">No restriction</option>
                <option value="yes_use_range">Only consider counts within a range</option>
            </param>
            <when value="no_use_range"/>
            <when value="yes_use_range">
                <param name="range_min" type="integer" value="" min="0"/>
                <param name="range_max" type="integer" value="" min="0"/>
            </when>
        </conditional>
        <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
            <param name="chromosome" type="text">
                <validator type="empty_field" />
            </param>
        </repeat>

        <expand macro="colormap" />

    </inputs>
    <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
        <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
        <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
    </outputs>

            </repeat>
            <repeat name="input_files">
                <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
                <param name="mlabel" value="second"/>
            </repeat>
            
            <param name="log1p" value="True"/>
            <param name="colormap" value="jet"/>
            <param name="method" value="spearman"/>
            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>

- Two contact matrices which are used for the correlation.
- Choice if pearson or spearman correlation should be used.
- log scale for the values
- Correlate full matrix or only specific chromosomes
- Correlate only within a given range.
- colormap to use:  Colormap_ 

Output
------

Pearson correlation

7:602a0c6f4bb0

            #if $method and $method is not None:
                --method $method
            #end if
            $log1p

            @USE_RANGE@

            #if $chromosomes:
                --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])#
            #end if

            #if $colormap:
                --colorMap $colormap
            #end if

            --outFileNameHeatmap ./heatmap.png
            --outFileNameScatter ./scatter.png
]]>
    </command>

            <option value="spearman">Spearman</option>
            <option selected="true" value="pearson">Pearson</option>
        </param>
        <param name="log1p" type="boolean" argument="--log1p"  truevalue="--log1p" falsevalue=""
            label="Use the log1p of the matrix values" help="(--log1p)" />

        <expand macro="use_range" />

        <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
            <param name="chromosome" type="text">
                <validator type="empty_field" />
            </param>
        </repeat>
        <expand macro="colormap" />
    </inputs>
    <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
        <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
        <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
    </outputs>

            </repeat>
            <repeat name="input_files">
                <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
                <param name="mlabel" value="second"/>
            </repeat>

            <param name="log1p" value="True"/>
            <param name="colormap" value="jet"/>
            <param name="method" value="spearman"/>
            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>

- Two contact matrices which are used for the correlation.
- Choice if pearson or spearman correlation should be used.
- log scale for the values
- Correlate full matrix or only specific chromosomes
- Correlate only within a given range.
- colormap to use:  Colormap_

Output
------

Pearson correlation