comparison hicPlotMatrix.xml @ 8:d398f5373c70 draft

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

7:f93a78bc045e

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #if str($pca_conditional.pca_type) == 'bedgraph':
            ln -s $pca_conditional.pca_bedgraph pca.bedgraph &&
            #set $pca = '--pca pca.bedgraph'
        #elif str($pca_conditional.pca_type) == 'bigwig':
            ln -s $pca_conditional.pca_bigwig pca.bw &&
            #set $pca = '--pca pca.bw'
        #elif str($pca_conditional.pca_type) == '':
            #set $pca = ''
        #end if
        
        @BINARY@

        <param argument="--vMax" type="float" optional="true" label="vMax"/>

        <conditional name="pca_conditional">
            <param name='pca_type' label='Datatype of eigenvector file' type='select'>
                <option value='' selected="true"></option>
                <option value='bedgraph'>bedgraph</option>
                <option value='bigwig'>bigwig</option>
            </param>
            <when value='' />
            <when value='bedgraph'>
                <param name='pca_bedgraph' type="data" format="bedgraph" 
                            label="Eigenvector file"/>
            </when>
            <when value='bigwig'>
                <param name='pca_bigwig'  type="data" format="bigwig" 
                            label="Eigenvector file"/>
            </when>
        </conditional>

        </test>
        <test>
            <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
            <param name="perChromosome" value="True"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value='bedgraph'/>
                <param name="pca_bedgraph" value="pca1.bedgraph"/>
            </conditional>
            <param name='colormap' value='hot'/>
            <param name="image_file_format" value="svg" />
            <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
        </test>

- What to show: 
- The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
- log / log1p of the values: It is recommended to use log1p.
- Colormaps_ for the heatmap. 
- vMin / vMax
- principal component: a bedgraph or bigwig file containing eigenvector information

Output
------

The contact matrix plotted for chromosome 1.

8:d398f5373c70

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        #if str($pca_conditional.pca_type) == 'bigwig':
            ln -s $pca_conditional.pca_bigwig pca.bw &&
            #set $pca = '--bigwig pca.bw'
        #elif str($pca_conditional.pca_type) == '':
            #set $pca = ''
        #end if
        
        @BINARY@

        <param argument="--vMax" type="float" optional="true" label="vMax"/>

        <conditional name="pca_conditional">
            <param name='pca_type' label='Datatype of eigenvector file' type='select'>
                <option value='' selected="true"></option>
                <option value='bigwig'>bigwig</option>
            </param>
            <when value='' />
            <when value='bigwig'>
                <param name='pca_bigwig'  type="data" format="bigwig" 
                            label="Eigenvector file"/>
            </when>
        </conditional>

        </test>
        <test>
            <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
            <param name="perChromosome" value="True"/>
            <conditional name="pca_conditional">
                <param name="pca_type" value='bigwig'/>
                <param name="pca_bigwig" value="pca1.bw"/>
            </conditional>
            <param name='colormap' value='hot'/>
            <param name="image_file_format" value="svg" />
            <output name="outFileName" file="small_matrix_50kb_pearson_pca1_plot.svg" ftype="svg" compare="sim_size" delta='35000'/>
        </test>

- What to show: 
- The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
- log / log1p of the values: It is recommended to use log1p.
- Colormaps_ for the heatmap. 
- vMin / vMax
- principal component: a bigwig file containing eigenvector information

Output
------

The contact matrix plotted for chromosome 1.