comparison hicPCA.xml @ 10:b0f5c30425c2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"

9:942b71f45588

        <token name="@BINARY@">hicPCA</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        hicPCA --matrix '$matrix_h5_cooler'

        --outputFileName pca1.$outputFormat pca2.$outputFormat
        --format $outputFormat

        && mv pca1.$outputFormat pca1
        && mv pca2.$outputFormat pca2

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param name='outputFormat' type='select' label="Output file format">
            <option value='bigwig' selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

    </inputs>
    <outputs>

        <data name="pca1" from_work_dir="pca1" format="bigwig" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: PC1">
            <filter>outputFormat == 'bigwig'</filter>
            <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>


    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
            <param name="outputFormat" value="bedgraph" />
            <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
            <output name="pca2" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/>
        </test>
        <test>
            <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>

            <param name="outputFormat" value="bigwig" />
            <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
            <output name="pca2" file="pca2.bw" ftype="bigwig" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Principal component analysis
============================

_________________

Output
------
Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``hicPlotTADs`` or ``hicPlotMatrix``.

For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.

.. image:: $PATH_TO_IMAGES/hicPCA.png
   :scale: 35 %

10:b0f5c30425c2

        <token name="@BINARY@">hicPCA</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
        @BINARY@ --matrix 'matrix.$matrix_h5_cooler.ext'

        @CHROMOSOME_LIST@

        --outputFileName pca1.$outputFormat pca2.$outputFormat
        --format $outputFormat

        #if $norm:
            $norm
        #end if

        #if $extra_track_conditional.extra_track_selection == 'gene_density':
            --extraTrack '$extra_track_conditional.extraTrack'
        #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
            --extraTrack '$extra_track_conditional.extraTrack'
            --histonMarkType '$extra_track_conditional.histonMarkType'
        #end if

        #if $pearsonMatrix:
            --pearsonMatrix pearson.$matrix_h5_cooler.ext
        #end if

        #if $obsexpMatrix:
            --obsexpMatrix obsexp.$matrix_h5_cooler.ext
        #end if

        && mv pca1.$outputFormat pca1
        && mv pca2.$outputFormat pca2
        #if $pearsonMatrix:
            && mv pearson.$matrix_h5_cooler.ext pearson
        #end if

        #if $obsexpMatrix:
            && mv obsexp.$matrix_h5_cooler.ext obsexp
        #end if

]]>
    </command>
    <inputs>
        <expand macro='matrix_h5_cooler_macro' />
        <param name='outputFormat' type='select' label="Output file format">
            <option value='bigwig' selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

        <expand macro="chromosome_list" />

        <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/>

        <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.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='norm' value='True'/>
            <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
============================

_________________

Output
------
Two files are outputed by **hicPCA**, one with the first (pca1) and one with the second (pca2) eigenvector as bigwig or bedgraph. These files can be plotted alongside Hi-C heatmaps, gene density or external datasets such as open chromatin or histone marks enrichment using ``pyGenomeTracks`` or ``hicPlotMatrix``.

For example, below you can find a ``hicPlotMatrix`` of the Pearson correlation matrix derived from a contact matrix for chromosome 6 in mouse computed with ``hicTransform`` (which is part of A/B compartments computation). The optional data track at the bottom shows the first eigenvector for A/B compartment obtained using **hicPCA**.

.. image:: $PATH_TO_IMAGES/hicPCA.png
   :scale: 35 %