comparison bamCompare.xml @ 18:5ea8782d650c draft

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17:ef65d6b68ccc

<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.2">
    <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        bamCompare

      #if $comparison.type=='subtract':
          #if $comparison.normalization.type=='rpkm':
            --normalizeUsingRPKM
          #elif $comparison.normalization.type=='1x':
            --normalizeTo1x $comparison.normalization.normalizeTo1x
          #end if
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
            #if $advancedOpt.smoothLength:
            --smoothLength '$advancedOpt.smoothLength'
            #end if

            #if str($advancedOpt.region.value) != '':
                --region '$advancedOpt.region'
            #end if

            $advancedOpt.doNotExtendPairedEnds
            $advancedOpt.ignoreDuplicates

                        <option value="no">Do not normalize or scale</option>
                    </param>
                    <when value="rpkm" />
                    <when value="no" />
                    <when value="1x">
                        <param name="normalizeTo1x" type="integer" value="2150570000"
                            label="Report normalized coverage to 1x sequenceing depth"
                            help ="Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
                    </when>
                </conditional>
            </when>
        </conditional>

        <param name="outFileFormat" type="select" label="Coverage file format">
            <option value="bigwig" selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>

            <when value="yes">

                <param name="smoothLength" type="integer" value="1" optional="true" min="1"
                    label="Smooth values using the following length (in bp)"
                    help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>

                <param name="region" type="text" value=""
                    label="Region of the genome to limit the operation to"
                    help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />

                <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
                    label="Do not extend paired ends"
                    help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


**Output files**:

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

-----

.. class:: infomark

    </help>
</tool>

18:5ea8782d650c

<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.3">
    <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <macros>
        <token name="@BINARY@">bamCompare</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        bamCompare

      #if $comparison.type=='subtract':
          #if $comparison.normalization.type=='rpkm':
            --normalizeUsingRPKM
          #elif $comparison.normalization.type=='1x':

            #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
            #else:
                --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
            #end if

          #end if
      #end if

      #if str(region).strip() != '':
          --region 'region'
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
            #if $advancedOpt.smoothLength:
            --smoothLength '$advancedOpt.smoothLength'
            #end if

            $advancedOpt.doNotExtendPairedEnds
            $advancedOpt.ignoreDuplicates

                        <option value="no">Do not normalize or scale</option>
                    </param>
                    <when value="rpkm" />
                    <when value="no" />
                    <when value="1x">
                        <expand macro="effectiveGenomeSize" />
                    </when>
                </conditional>
            </when>
        </conditional>

        <param name="outFileFormat" type="select" label="Coverage file format">
            <option value="bigwig" selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>

            <when value="yes">

                <param name="smoothLength" type="integer" value="1" optional="true" min="1"
                    label="Smooth values using the following length (in bp)"
                    help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>

                <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
                    label="Do not extend paired ends"
                    help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


You can find more details in the `bamCompare wiki`_.

.. _bamCompare wiki: 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.

-----

@REFERENCES@

    </help>
</tool>