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<tool id="QDNAseq-regioning" name="QDNAseq-regioning" version="0.0.1" force_history_refresh="True">
  
  <requirements>
    
    <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command -->
    <!-- <requirement type="package" version="3.1.0">R</requirement> -->
    <!-- <requirement type="package" version="1.2.2">qdnaseq</requirement> -->
    
  </requirements>

  <description>Perform regioning on QDNAseq data</description>

  <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) -->
  <command interpreter="Rscript"> 
    QDNAseq-regioning.R 
    $cfg
  </command>

  <version_command interpreter="Rscript">QDNAseq-version.R</version_command>

  <stdio>
    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
    <exit_code range="1:" level="fatal" description="R script finished too early, check log" />
  </stdio>
  
  <inputs>
    
    <!-- ==================== -->
    <!-- General inputs -->
    <!-- ==================== -->
    
    <!-- Job name: must contain non-whitespace chars -->
    <param name="output_name" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
      <!-- <validator type="empty_field" /> -->
      <validator type="regex" message="No whitespace characters allowed">^[^\s\\]*$</validator>
    </param>

    <!-- ==================== -->
    <!-- Input RDS -->
    <!-- ==================== -->
    <param name="rds_file_path" type="data" optional="False" format="rds" label="Input RDS file" help="RDS file should contain a QDNAseq R object (output of QDNAseq tool)" />

    <param name="av_error" size="10" type="float" value="0.00001" optional="False" label="Average Error" help="By default low so that most if not all possible breakpoints in the data are kept, output will then contain smaller regions." />
    
  </inputs>

  <!-- ==================== -->
  <!-- Config file to pass params to R script -->
  <!-- ==================== -->
  <configfiles>
    <configfile name="cfg">
## Desc: this file is sourced in QDNAseq-region.R wrapper script
##  as means to pass all galaxy params to R

"${output_name}" -> outputName
"${output_file}" -> outputFile
"${rds_file_path}" -> rdsFilePath
as.double( "${av_error}" ) -> avError

    </configfile>
  </configfiles>

  <!-- ==================== -->
  <!-- One text file as output -->
  <!-- ==================== -->
  <outputs>
    <data format="tabular" name="output_file" label="QDNAseq: ${output_name} regions file" />
  </outputs>

  <help>

**Introduction**

This tool is a wrapper for the "CGHregions" function of the R Bioconductor package CGHregions_ and works on objects of the R bioconductor package QDNAseq_

-----

**What it does**

**Input:** The input for this tool is a QDNAseq R object in RDS (R data structure) format, an (optional) output file of the QDNAseq galaxy tool. **Output:** Running this regioning tool overlaps the called called segments from all samples present in the input object. The output contains the merged segments with their call values for each sample.

-----

**Output examples**

*Example TSV output:*

::

 Chromosome  Start    End      Nclone  AveDist  sample1  sample2
 1           6000001  7000000  42      0        1        -1
 1           7000001  8000000  11      0        0        -1

-----

.. class:: warningmark

As there is no R 3.1.0 galaxy-package yet (a requirement for QDNAseq) that works with all requirements, 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 (>= 1.2.2). In case the path to this R installation is not "R", also the wrapper xml must be updated to include the correct path during installation of this tool.

-----

**Citation**

For the underlying QDNAseq R package please cite: 
Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG and Ylstra B (2014). “DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.” Genome Research. doi:10.1101/gr.175141.114.

See also the bioconductor documentation of QDNAseq_ and CGHregions_

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

.. image:: LGG150_copynumber.png
.. image:: LGG150_copynumberSegmented.png

  </help>

</tool>