annotate chicViewpoint.xml @ 6:dbfd2cfc0f66 draft

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

<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>computes viewpoints with the given reference points and a background model.</description>
    <macros>
        <token name="@BINARY@">chicViewpoint</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        #import re

        mkdir interactionFiles &&
        #for $m in $matrix_h5_cooler_multiple:
            #set identifier = @ESCAPE_IDENTIFIER_M@
            ln -s '$m' '$identifier' &&
        #end for
        #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])

        @BINARY@
            --matrices $m
            --range $rangeUpstream $rangeDownstream
            --referencePoints '$referencePoints'
            --averageContactBin $averageContactBin
            --fixateRange $fixateRange
            --decimalPlaces $decimalPlaces
            --threads @THREADS@
            --backgroundModelFile '$backgroundModelFile'
            --outputFolder interactionFiles
            $writeFileNamesToFile
        
        #if $tar:
            && cd interactionFiles
            && tar -cvf ../viewpoints.tar .
            && cd ..
            && rm -rf interactionFiles
        #end if

    ]]>    </command>
    <inputs>
        <expand macro="matrix_h5_cooler_multiple_macro" />

        <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." />
        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />

        <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
        <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' />
        <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' />
        <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.' />

        <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" help="Set this parameter if you want to use the batch processing mode for the further analysis." />
        <param name='tar' type='boolean' checked="false" label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." />

    </inputs>
    <outputs>
        <collection name="interactionFilesCollection" type="list" label="Interaction files">
            <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
        </collection>
        <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
            <filter>writeFileNamesToFile</filter>
        </data>
        <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
            <filter>tar</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
            <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
            <param name="backgroundModelFile" value="cHi-C/background.txt" />
            <param name="fixateRange" value="500000" />
            <param name="rangeUpstream" value="200000" />
            <param name="rangeDownstream" value="200000" />
            <param name="writeFileNamesToFile" value="True" />

            <output_collection name="interactionFilesCollection" type="list" count="6">
                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3" />
                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3" />
                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
                    <assert_contents>
                        <has_text text="18895000" />
                        <has_text text="chr1" />
                        <has_text text="Tfap2d" />
                        <has_text text="interactions" />
                        <has_text text="472.0" />
                    </assert_contents>
                </element>
                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3" />
                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
                    <assert_contents>
                        <has_text text="14100000" />
                        <has_text text="chr1" />
                        <has_text text="Eya1" />
                        <has_text text="interactions" />
                        <has_text text="832.0" />
                    </assert_contents>
                </element>
                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
                    <assert_contents>
                        <has_text text="4455000" />
                        <has_text text="chr1" />
                        <has_text text="Sox17" />
                        <has_text text="interactions" />
                        <has_text text="978.0" />
                        <has_text text="-30000" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
        </test>
        <test>
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
            <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
            <param name="backgroundModelFile" value="cHi-C/background.txt" />
            <param name="fixateRange" value="500000" />
            <param name="rangeUpstream" value="200000" />
            <param name="rangeDownstream" value="200000" />
            <param name="writeFileNamesToFile" value="False" />
            <output_collection name="interactionFilesCollection" type="list" count="6">
                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3" />
                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3" />
                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
                    <assert_contents>
                        <has_text text="18893000" />
                        <has_text text="chr1" />
                        <has_text text="Tfap2d" />
                        <has_text text="interactions" />
                        <has_text text="472.0" />
                    </assert_contents>
                </element>
                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3" />
                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
                    <assert_contents>
                        <has_text text="14103000" />
                        <has_text text="chr1" />
                        <has_text text="Eya1" />
                        <has_text text="interactions" />
                        <has_text text="832.0" />
                        <has_text text="-199000" />
                    </assert_contents>
                </element>
                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
                    <assert_contents>
                        <has_text text="4455000" />
                        <has_text text="chr1" />
                        <has_text text="Sox17" />
                        <has_text text="interactions" />
                        <has_text text="978.0" />
                        <has_text text="-30000" />
                    </assert_contents>
                </element>
            </output_collection>
            <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
        </test>
        <test>
            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
            <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
            <param name="backgroundModelFile" value="cHi-C/background.txt" />
            <param name="fixateRange" value="500000" />
            <param name="rangeUpstream" value="200000" />
            <param name="rangeDownstream" value="200000" />
            <param name="writeFileNamesToFile" value="True" />
            <param name='tar' value='True' />
            <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' />
            <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
        </test>
    </tests>
    <help><![CDATA[

Compute viewpoints for all given reference points
=================================================

Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
are named by the name of the reference point, the sample name and  the location of the reference point:

gene_matrix_name_chr_start_end.txt

If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.

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

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
]]>    </help>
    <expand macro="citations" />
</tool>