CopyNumberDeletion.xml

<?xml version="1.0"?>
<tool id="CopyNumberDeletion" name="Copy Number Deletion" version="1.0" hidden="false">
  <description>Identify copy number deletions </description>
  
  <requirements>
      <requirement type="package" version="3.1.2">R</requirement>
      <requirement type="package" version="7.3-40">MASS</requirement>
      <requirement type="package" version="1.7.2">calibrate</requirement>
      <requirement type="package" version="1.3.0">optparse</requirement>
      <requirement type="package" version="3.5-11">plotrix</requirement>
      <requirement type="package" version="0.3.1">DBI</requirement>
      <requirement type="package" version="0.10.2">RMySQL</requirement>
      <requirement type="package" version="1.7-12">zoo</requirement>
      <requirement type="package" version="1.0.0">CopyNumberDeletion</requirement>
  </requirements>
  
 <command >
     Rscript CopyNumberDeletion.R  --s_name $sample_name --c_name $c_sample_name --s_pileup $s_pileup --s_bwa $s_bwa --s_bowtie $s_bowtie --c_pileup $c_pileup --c_bwa $c_bwa --c_bowtie $c_bowtie --platform $platform --ordered_genes $ordered_genes --db_h localhost --db_u onson001 --db_p masara15 --db_d fairview_2013_09_25
 </command>
 
  <inputs>
    <param name="sample_name" type="text"  value="11_05910" label="sample name" />
    <param name="s_pileup" format="pileup" type="data" label="sample coverage pileup"/>
    <param name="s_bwa" format="pileup" type="data" label="sample bwa pileup"/>
    <param name="s_bowtie" format="pileup" type="data" label="sample bowtie pileup"/>
    <param name="c_sample_name" type="text"  value="07_2151" label="control name" />
    <param name="c_pileup" format="pileup" type="data" label="control coverage pileup"/>
    <param name="c_bwa" format="pileup" type="data" label="control bwa pileup"/>
    <param name="c_bowtie" format="pileup" type="data" label="control bowtie pileup"/>
    <param name="platform" type="text"  value="TruSightOne" label="platform"/>
    <param name="ordered_genes" format="txt" type="data" label="ordered genes"/>
  </inputs>
 
  <outputs>
      <data name="cnv" format="txt" label="cnv" from_work_dir="cnv.txt"/>
      <data name="raw_data" format="txt" label="raw_data" from_work_dir="raw_data.txt"/>
      <data name="CoveragePlots" format="pdf" label="CoveragePlots" from_work_dir="CoveragePlots.pdf"/>
  </outputs>
 
  <help>
    **What it does**
    
    Identify copy number deletions.
  
  </help>
</tool>