comparison chicViewpoint.xml @ 4:78b70d78a596 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"

3:8fb584526458

<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>computes viewpoints with the given reference points and a background model.</description>
    <macros>
        <token name="@BINARY@">chicViewpoint</token>
        <import>macros.xml</import>
    </macros>

            --decimalPlaces $decimalPlaces
            --threads @THREADS@
            --backgroundModelFile '$backgroundModelFile'
            --outputFolder interactionFiles
            $writeFileNamesToFile

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

        <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."/>
    </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>
    </outputs>
    <tests>
        <test>
           <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>

                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
            </output_collection>
            <!-- <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
=================================================

4:78b70d78a596

<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.1">
    <description>computes viewpoints with the given reference points and a background model.</description>
    <macros>
        <token name="@BINARY@">chicViewpoint</token>
        <import>macros.xml</import>
    </macros>

            --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="--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"/>

                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
            </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
=================================================