comparison QDNAseq.xml @ 43:327b8830d49f draft

Uploaded

42:4351c7715275

      <option value="30">30kb</option>
      <option value="15">15kb</option>
      <option value="5">5kb</option>
      <option value="1">1kb</option>
    </param>
    <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
      <option value="TRUE">yes</option>
      <option value="FALSE">no</option>
    </param>
    <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy">
      <option value="SR50">Single Read 50bp</option>
      <!-- <option value="PE1000">PairedEnd1000</option> -->
    </param>

    <!-- ==================== -->
    <!-- Input BAMs -->
    <!-- ==================== -->
    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select all BAM files to include in the analysis" />

    <!-- ==================== -->
    <!-- This section contains galaxy history output settings -->
    <!-- ==================== -->
    <conditional name="extra_history_outputs">
      <param name="show" type="select" label="Show additional history outputs">
        <option value="NO">Only output Report to history</option>
        <option value="YES">Select additional history outputs</option>
      </param>
      <when value="YES">
        <param name="readcounts_rds" type="select" label="Also output readcounts RDS (R object) to history">

      <param name="show" type="select" label="Show advanced options">
        <option value="no">no</option>
        <option value="yes">yes</option>
      </param>
      <when value="yes">
        
        <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below">
          <option value="sdundo">sdundo</option>
          <option value="prune">prune</option>
          <option value="none">none</option>

          <option value="TRUE">yes</option>
        </param>
      </when>
      <!-- need to set defaults because params are passed to R anyway -->
      <when value="no">
        <param name="undoSD" type="hidden" value="1" />
        <param name="undo_splits" type="hidden" value="sdundo" />
        <param name="blacklist" type="hidden" value="TRUE" />
        <param name="mappability" type="hidden" value="0" />
        <param name="debug" type="hidden" value="FALSE" />

as.integer( "${binSize}" ) -> binSize
"${experimentType}" -> experimentType
"${jobName}" -> outputName

## extra params
as.logical( "${doCall}" ) -> doCall
"${htmlFile}" -> outputHtml
"${htmlFile.files_path}" -> outputPath
"${use_own_binannotation.binannotation_file}" -> binAnnotations

## advanced options
as.double( "${advanced.undoSD}" ) -> undoSD
as.logical( "${advanced.debug}" ) -> debug
as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
as.integer( "${advanced.mappability}" ) -> mappabilityCutoff
"${advanced.undo_splits}" -> undoSplits

.. _QDNAseq: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html

It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.

-----

.. class:: warningmark

As there is no R 3.1.0 package yet which is required, the **dependencies** need to be installed by hand and available to the galaxy user: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5)

.. class:: warningmark

The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups.

.. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html


.. image:: LGG150_copynumber_example.png
  </help>

</tool>

43:327b8830d49f

      <option value="30">30kb</option>
      <option value="15">15kb</option>
      <option value="5">5kb</option>
      <option value="1">1kb</option>
    </param>

    <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy">
      <option value="SR50">Single Reads of 50bp</option>
      <!-- <option value="PE1000">PairedEnd1000</option> -->
    </param>

    <!-- ==================== -->
    <!-- Input BAMs -->
    <!-- ==================== -->
    <param name="bams" type="data" multiple="true" optional="false" format="bam" label="Input BAMs" help="Select the BAM files to analyze" />

    <!-- ==================== -->
    <!-- This section contains galaxy history output settings -->
    <!-- ==================== -->
    <conditional name="extra_history_outputs">
      <param name="show" type="select" label="Optional history outputs">
        <option value="NO">Only output Report to history</option>
        <option value="YES">Select additional history outputs</option>
      </param>
      <when value="YES">
        <param name="readcounts_rds" type="select" label="Also output readcounts RDS (R object) to history">

      <param name="show" type="select" label="Show advanced options">
        <option value="no">no</option>
        <option value="yes">yes</option>
      </param>
      <when value="yes">
        <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)">
          <option value="TRUE">yes</option>
          <option value="FALSE">no</option>
        </param>
        
        <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below">
          <option value="sdundo">sdundo</option>
          <option value="prune">prune</option>
          <option value="none">none</option>

          <option value="TRUE">yes</option>
        </param>
      </when>
      <!-- need to set defaults because params are passed to R anyway -->
      <when value="no">
        <param name="doCall" type="hidden" value="TRUE" />
        <param name="undoSD" type="hidden" value="1" />
        <param name="undo_splits" type="hidden" value="sdundo" />
        <param name="blacklist" type="hidden" value="TRUE" />
        <param name="mappability" type="hidden" value="0" />
        <param name="debug" type="hidden" value="FALSE" />

as.integer( "${binSize}" ) -> binSize
"${experimentType}" -> experimentType
"${jobName}" -> outputName

## extra params
"${htmlFile}" -> outputHtml
"${htmlFile.files_path}" -> outputPath
"${use_own_binannotation.binannotation_file}" -> binAnnotations

## advanced options
as.logical( "${advanced.doCall}" ) -> doCall
as.double( "${advanced.undoSD}" ) -> undoSD
as.logical( "${advanced.debug}" ) -> debug
as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins
as.integer( "${advanced.mappability}" ) -> mappabilityCutoff
"${advanced.undo_splits}" -> undoSplits

.. _QDNAseq: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html

It determines the copy number state of human chromosomes 1 - 22 for (shallow coverage) whole genome sequencing data.

For questions/remarks about the galaxy part of this tool, see contact form here_

.. _here: http://www.stefs.nl/wp/contact

-----

.. class:: warningmark

As there is no R 3.1.0 package yet (which is required), the **dependencies** need to be installed by hand and available to the user under which galaxy runs: R (3.1.0) and bioconductor package QDNAseq (>= 1.0.5)

.. class:: warningmark

The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups.

.. _package: http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html


.. image:: LGG150_copynumber_example.png
.. image:: LGG150_calls_example.png
  </help>

</tool>