comparison hicPCA.xml @ 14:3b5b54ed6392 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"

13:0ba4f56a3613

<tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>compute the principal components for A / B compartment analysis</description>
    <macros>
        <token name="@BINARY@">hicPCA</token>
        <import>macros.xml</import>
    </macros>

            <option value="bedgraph">bedgraph</option>
        </param>

        <expand macro="chromosome_list" />

        <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation'/>
        <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed'/>

        <conditional name="extra_track_conditional">
            <param name='extra_track_selection' label='Extra track type' type='select'>
                <option value='' selected='true'>No track</option>
                <option value='gene_density'>Gene density</option>
                <option value='histon_mark'>Histon mark coverage</option>
            </param>
            <when value='gene_density' >
                <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign'/>
            </when>
            <when value='histon_mark'>
                <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign'/>
                <param name='histonMarkType' type='select' label="Histon mark type">
                    <option value='active' selected="true">active</option>
                    <option value="inactive">inactive</option>
                </param>
            </when>
            <when value='' />
        </conditional>

        <param name='pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix'/>
        <param name='obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix'/>

    </inputs>
    <outputs>
        <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1">
            <change_format>
                <when input="outputFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>
        <data name="pca2" from_work_dir="pca2" format="bigwig"  label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2">
            <change_format>
                <when input="outputFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>

        <data name="pearson_outfile" from_work_dir="pearson" format="cool">
            <filter>pearsonMatrix</filter>
            <change_format>
                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
            </change_format>
        </data>
        <data name="obsexp_outfile" from_work_dir="obsexp" format="cool">
            <filter>obsexpMatrix</filter>
            <change_format>
                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
            <param name="outputFormat" value="bigwig" />
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value=""/>
            </conditional>

            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
            <param name="outputFormat" value="bigwig" />
            <param name="ligation_factor" value="True" />

            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value=""/>
            </conditional>

            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
            <param name="outputFormat" value="bigwig" />
            <param name="ignoreMaskedBins" value="True" />

            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value=""/>
            </conditional>

            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/>
            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000'/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
            <param name="outputFormat" value="bigwig" />
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="gene_density"/>
                <param name="extraTrack" value="dm3_genes.bed.gz" />
            </conditional>

            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrX"/>
            </repeat>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrXHet"/>
            </repeat>

            <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
            <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>

            <param name="outputFormat" value="bigwig" />
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value=""/>
            </conditional>
            <param name='pearsonMatrix' value='True'/>
            <param name='obsexpMatrix' value='True'/>

            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrX"/>
            </repeat>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrXHet"/>
            </repeat>

            <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000'/>
            <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000'/>

            <output name="pearson_outfile" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix'/>
                </assert_contents>
            </output>
            <output name="obsexp_outfile" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Principal component analysis
============================

`Lieberman-Aiden et al. (2009)`_ demonstrated that open and closed chromatin domains throughout the genome occupy different spatial compartments in the nucleus, defined as A (activate) and B (inactive) compartments.

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
]]></help>
    <expand macro="citations" />
</tool>

14:3b5b54ed6392

<tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>compute the principal components for A / B compartment analysis</description>
    <macros>
        <token name="@BINARY@">hicPCA</token>
        <import>macros.xml</import>
    </macros>

            <option value="bedgraph">bedgraph</option>
        </param>

        <expand macro="chromosome_list" />

        <param name='ligation_factor' type='boolean' truevalue='--ligation_factor' label='Multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation' />
        <param name='ignoreMaskedBins' type='boolean' truevalue='--ignoreMaskedBins' label='This option removes the masked bins before the PCA is computed' />

        <conditional name="extra_track_conditional">
            <param name='extra_track_selection' label='Extra track type' type='select'>
                <option value='' selected='true'>No track</option>
                <option value='gene_density'>Gene density</option>
                <option value='histon_mark'>Histon mark coverage</option>
            </param>
            <when value='gene_density' >
                <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histon marks to flip sign' />
            </when>
            <when value='histon_mark'>
                <param name='extraTrack' type='data' format='bed,bigwig' label='Correlate PCA with e.g. gene density or histon marks to flip sign' />
                <param name='histonMarkType' type='select' label="Histon mark type">
                    <option value='active' selected="true">active</option>
                    <option value="inactive">inactive</option>
                </param>
            </when>
            <when value='' />
        </conditional>
        <param argument='--pearsonMatrix' type='boolean' truevalue='--pearsonMatrix' falsevalue='' label='Return internally used Pearson matrix' />
        <param argument='--obsexpMatrix' type='boolean' truevalue='--obsexpMatrix' falsevalue='' label='Return internally used observed / expected matrix' />

    </inputs>
    <outputs>
        <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1">
            <change_format>
                <when input="outputFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>
        <data name="pca2" from_work_dir="pca2" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC2">
            <change_format>
                <when input="outputFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>

        <data name="pearson_outfile" from_work_dir="pearson" format="cool">
            <filter>pearsonMatrix</filter>
            <change_format>
                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
            </change_format>
        </data>
        <data name="obsexp_outfile" from_work_dir="obsexp" format="cool">
            <filter>obsexpMatrix</filter>
            <change_format>
                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
            <param name="outputFormat" value="bigwig" />
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="" />
            </conditional>

            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
            <param name="outputFormat" value="bigwig" />
            <param name="ligation_factor" value="True" />

            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="" />
            </conditional>

            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='40000' />
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
            <param name="outputFormat" value="bigwig" />
            <param name="ignoreMaskedBins" value="True" />

            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="" />
            </conditional>

            <output name="pca1" file="hicPCA/pca1_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' />
            <output name="pca2" file="hicPCA/pca2_test1.bw" ftype="bigwig" compare="sim_size" delta='60000' />
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
            <param name="outputFormat" value="bigwig" />
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="gene_density" />
                <param name="extraTrack" value="dm3_genes.bed.gz" />
            </conditional>

            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrX" />
            </repeat>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrXHet" />
            </repeat>

            <output name="pca1" file="hicPCA/pca1_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' />
            <output name="pca2" file="hicPCA/pca2_test2.bw" ftype="bigwig" compare="sim_size" delta='40000' />
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />

            <param name="outputFormat" value="bigwig" />
            <conditional name="extra_track_conditional">
                <param name="extra_track_selection" value="" />
            </conditional>
            <param name='pearsonMatrix' value='True' />
            <param name='obsexpMatrix' value='True' />

            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrX" />
            </repeat>
            <repeat name="chromosome_list">
                <param name="chromosomes" value="chrXHet" />
            </repeat>

            <output name="pca1" file="hicPCA/pca1_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' />
            <output name="pca2" file="hicPCA/pca2_test3.bw" ftype="bigwig" compare="sim_size" delta='40000' />

            <output name="pearson_outfile" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix' />
                </assert_contents>
            </output>
            <output name="obsexp_outfile" ftype="h5">
                <assert_contents>
                    <has_h5_keys keys='intervals,matrix' />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Principal component analysis
============================

`Lieberman-Aiden et al. (2009)`_ demonstrated that open and closed chromatin domains throughout the genome occupy different spatial compartments in the nucleus, defined as A (activate) and B (inactive) compartments.

| For more information about HiCExplorer please consider our documentation on readthedocs.io_

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
]]>    </help>
    <expand macro="citations" />
</tool>