comparison bamCoverage.xml @ 6:c5847db0cb41 draft

Uploaded

5:1f312af2f8db

<tool id="bamCoverage" name="bamCoverage" version="1.0">
  <description>Given a BAM file, generates a coverage bigwig file.  Multiple options available to count reads and normalize coverage.</description>
  <requirements>
    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
    <requirement type="package" version="0.1">ucsc_tools</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
  </requirements>
  <command>
  bamCoverage

  ##ToDo

  #elif $scaling.type=='1x':
    --normalizeTo1x $scaling.normalizeTo1x
  #elif $scaling.type=='own':
    --scaleFactor $scaling.scaleFactor
  #end if
  
  #if $advancedOpt.showAdvancedOpt == "yes":
    #if $advancedOpt.smoothLength:
      --smoothLength '$advancedOpt.smoothLength'
    #end if

  #end if
  </command>

  <inputs>
    <param name="bamInput" format="bam" type="data" label="Input BAM file"
       help="The BAM file must be sorted and indexed."/>

    <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. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>

      <when value="own">
        <param name="scaleFactor" type="float" value="1" size="3" 
           label="Scale factor to multiply all values" />
        </when>
    </conditional>

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

            label="Ignore duplicates"
            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 

          <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
        </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="bigwig" name="outFileName">

-----

.. class:: infomark

If you would like to give us feedback or you run into any trouble, please sent an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.


.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _Fidel Ramirez: [e-mail]

</help>
</tool>

6:c5847db0cb41

<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
  <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage.</description>
  <requirements>
    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
    <requirement type="package" version="0.1">ucsc_tools</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
    <requirement type="package" >deepTools</requirement>
  </requirements>
  <command>
  bamCoverage

  ##ToDo

  #elif $scaling.type=='1x':
    --normalizeTo1x $scaling.normalizeTo1x
  #elif $scaling.type=='own':
    --scaleFactor $scaling.scaleFactor
  #end if

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

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

  #end if
  </command>

  <inputs>
    <param name="bamInput" format="bam" type="data" label="Input BAM file"
       help="The BAM file must be sorted."/>

    <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. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>

      <when value="own">
        <param name="scaleFactor" type="float" value="1" size="3" 
           label="Scale factor to multiply all values" />
        </when>
    </conditional>

    <!--
    Not yet supported.
    <param name="ignoreForNormalization" type="text" value="" size="50"
        label="regions that should be excluded for calculating the scaling factor"
        help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
    -->

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

            label="Ignore duplicates"
            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 

          <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
        </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="bigwig" name="outFileName">

-----

.. class:: infomark

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.


.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de

</help>
</tool>