comparison bamCompare.xml @ 6:0da0ae5c854e draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

5:7aa5951c56b7

        <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
            help="The BAM file must be sorted."/>
        <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
            help="The BAM file must be sorted."/>

        <param argument="--binSize" type="integer" value="50" min="1"
            label="Bin size in bp"
            help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported.
                If only half a fragment overlaps, this fraction will be reported."/>

        <conditional name="scaling">
            <param name="method" type="select"
                label="Method to use for scaling the largest sample to the smallest">
                <option value="readCount" selected="true">read count</option>
                <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
                <option value="own">enter own scaling factors</option>
            </param>

                <expand macro="scaleFactors" />
            </when>
        </conditional>

        <conditional name="comparison">
            <param name="type" type="select"
                label="How to compare the two files"
                help="The default is to output the log2ratio between the two samples.
                The reciprocal ratio returns the negative of the inverse of the ratio if
                the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
                <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


You can find more details on the bamCompare doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamCompare.html


**Output files**:

- same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.

6:0da0ae5c854e

        <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
            help="The BAM file must be sorted."/>
        <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
            help="The BAM file must be sorted."/>

        <param argument="--binSize" type="integer" value="50" min="1" 
            label="Bin size in bp"
            help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported.
                If only half a fragment overlaps, this fraction will be reported."/>

        <conditional name="scaling">
            <param name="method" type="select" 
                label="Method to use for scaling the largest sample to the smallest">
                <option value="readCount" selected="true">read count</option>
                <option value="SES">signal extraction scaling (SES), check the bamFingerprint plot before using it!</option>
                <option value="own">enter own scaling factors</option>
            </param>

                <expand macro="scaleFactors" />
            </when>
        </conditional>

        <conditional name="comparison">
            <param name="type" type="select" 
                label="How to compare the two files"
                help="The default is to output the log2ratio between the two samples.
                The reciprocal ratio returns the negative of the inverse of the ratio if
                the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
                <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare


**Output files**:

- same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.