view c_rpkm.xml @ 16:558f04d13648 draft

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<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0">
  <description></description>
  <command>
     mkdir rpkm_dir;
#for $input_bam in $inputs:
	#if str($input_bam.label.value) != "":
	     ln -s ${input_bam.inputFile} ${$input_bam.label.value}.bam;
	     ln -s ${input_bam.inputFile.metadata.bam_index} ${$input_bam.label.value}.bam.bai;
	     python \${CONIFER_PATH}/conifer.py rpkm 
	     --probes $probesFile 
	     --input ${$input_bam.label.value}.bam
	     --output rpkm_dir/${$input_bam.label.value}.txt;
	#else
	     ln -s ${input_bam.inputFile} ${input_bam.inputFile.dataset.name}.bam;
	     ln -s ${input_bam.inputFile.metadata.bam_index} ${input_bam.inputFile.dataset.name}.bam.bai;
	     python \${CONIFER_PATH}/conifer.py rpkm 
	     --probes $probesFile 
	     --input ${input_bam.inputFile.dataset.name}.bam
	     --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt;
	#end if
#end for
     python \${CONIFER_PATH}/conifer.py analyze 
     --probes $probesFile 
     --rpkm_dir rpkm_dir  
     --output $outputFile 
     --svd $svd 
     2&gt;&amp;1;
  </command>
  <inputs>
    <param format="bed" name="probesFile" type="data" label="Target regions (BED)" />
    <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
      <param format="bam" name="inputFile" type="data" label="BAM file" />
      <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
        <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
      </param>
    </repeat>
    <param name="svd" type="integer" value="2" label="SVD" />
  </inputs>
  <outputs>
    <data format="hdf5" name="outputFile" label="${tool.name} on ${on_string}: hdf5" />
  </outputs>
  <help>

.. class:: warningmark

**Warning about SVD**

The SVD value must be less than the number of samples.

E.g.: if the number of samples is 3, the value of SVD must be 2 or less.

**What it does**

This tool calculates RPKM for each BAM file and analyzes them, afterward it creates a unique HDF5 file containing all SVD-ZRPKM values,
probes and samples for downstream analysis with 'CoNIFER CNV caller' and 'CoNIFER plot'.

**License and citation**

This Galaxy tool is Copyright © 2015 `CRS4 Srl.`_ and is released under the `MIT license`_.

.. _CRS4 Srl.: http://www.crs4.it/
.. _MIT license: http://opensource.org/licenses/MIT

You can use this tool only if you agree to the license terms of: `CoNIFER`_.

.. _CoNIFER: http://conifer.sourceforge.net/

If you use this tool, please cite:

- |Cuccuru2014|_
- |Krumm2012|_.

.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
.. |Krumm2012| replace::  Krumm, N., Sudmant, P. H., Ko, A., O'Roak, B. J., Malig, M., Coe, B. P., NHLBI Exome Sequencing Project, Quinlan, A. R., Nickerson, D. A., Eichler, E. E. (2012) Copy number variation detection and genotyping from exome sequence data. *Genome Res.* 22(8), 1525-1532
.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu135</citation>
    <citation type="doi">10.1101/gr.138115.112</citation>
  </citations>
</tool>