comparison bamCorrelate.xml @ 52:c0a054f2eff8 draft

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51:329e8411cc51

    <macros>
        <token name="@BINARY@">bamCorrelate</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        #set files=[]
        #set labels=[]

        @multiple_input_bams@

                --zMax $mode.advancedOpt.zMax
            #end if
            --colorMap '$mode.advancedOpt.colorMap'

        #end if
    </command>

    <inputs>
        <expand macro="multiple_input_bams" />

        <param name="fragmentLength" type="integer" value="300" min="1"
            label="Length of the average fragment size"
            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>

        <param name="corMethod" type="select" label="Correlation method">
            <option value="spearman" selected="True">Spearman</option>
            <option value="pearson">Pearson</option>
        </param>

                        deviations from the median."/>

                <expand macro="bamCorrelate_mode_actions" />
            </when>
            <when value="BED-file">
                <param name="region_file" type="data" format="bed" label="Region file in BED format" help="Correlation is computed for the number of reads that overlap such regions."/>
                <expand macro="bamCorrelate_mode_actions" />
            </when>

        </conditional>

        <conditional name="output">
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>

                output['saveCorMatrix'] is True
            ))
            </filter>
        </data>
    </outputs>
    <help>

**What it does**

This tool is useful to assess the overall similarity of different BAM files. A typical application
is to check the correlation between replicates or published data sets.

-----

@REFERENCES@

    </help>
    <expand macro="citations" />
</tool>

52:c0a054f2eff8

    <macros>
        <token name="@BINARY@">bamCorrelate</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
<![CDATA[
        #set files=[]
        #set labels=[]

        @multiple_input_bams@

                --zMax $mode.advancedOpt.zMax
            #end if
            --colorMap '$mode.advancedOpt.colorMap'

        #end if
]]>
    </command>

    <inputs>
        <expand macro="multiple_input_bams" />

        <param name="fragmentLength" type="integer" value="200" min="1"
            label="Length of the average fragment size"
            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length. (--fragmentLength)"/>

        <param name="corMethod" type="select" label="Correlation method">
            <option value="spearman" selected="True">Spearman</option>
            <option value="pearson">Pearson</option>
        </param>

                        deviations from the median."/>

                <expand macro="bamCorrelate_mode_actions" />
            </when>
            <when value="BED-file">
                <param name="region_file" type="data" format="bed"
                    label="Region file in BED format"
                    help="Correlation is computed for the number of reads that overlap such regions."/>
                <expand macro="bamCorrelate_mode_actions" />
            </when>
        </conditional>

        <conditional name="output">
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>

                output['saveCorMatrix'] is True
            ))
            </filter>
        </data>
    </outputs>
    <tests>
        <test>
            <repeat name="input_files">
                <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
            </repeat>
            <repeat name="input_files">
                <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
            </repeat>
            <param name="modeOpt" value="bins" />
            <param name="binSize" value="10" />
            <param name="showOutputSettings" value="no" />
            <output name="outFileName" file="bamCorrelate_result1.png" ftype="png" compare="sim_size" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool is useful to assess the overall similarity of different BAM files. A typical application
is to check the correlation between replicates or published data sets.

-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>