view ClusterFast.xml @ 10:6006459b580a draft

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<tool id="ClusterFast" name="ClusterFast" version="0611">
  <description></description>
  <command interpreter="perl">
     run_cf0611.pl 
    
      ## input files
      	-b $input1
      	-t $input2
	
      ## references 
	-p "${indexes.fields.path}" 
		
      ## output files
      	-o $__new_file_path__  ## use galaxy temp dir for automatic cleanup.
	-c $contigs
	-y $bp1
	-z $bp2
	 

      ## run parameters
      	-r 0 ## clean up not needed, as this is in galaxy tmp.
      	-m1 $m1
	-m2 $m2
	-d $distance
     > $runlog
  </command>
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
    <requirement type="package" version="latest">novoalign</requirement>
    <requirement type="package" version="latest">velvet</requirement>
    <requirement type="package" version="latest">blat_server</requirement>
    <requirement type="package" version="0611">clusterfast</requirement>
  </requirements>
  <inputs>
        <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads." />
        <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" />
        <param name="m1" type="integer" value="2" label="Supporting Discordant Read Pairs" help="Default: 2"  />  
	<param name="m2" type="integer" value="1" label="Supporting Split Reads" help="Default: 1" />
	<param name="distance" type="integer" value="50000" label="Max Distance From Target To Search" help="Default: 50000" />
	<param name="indexes" type="select" label="Reference Genome" help="Select the correct genome build" >
		<options from_data_table="clusterfast" >
			<filter type="sort_by" column="2" />
			<validator type="no_options" message="No indexes are available" />
		</options>
	</param>
  </inputs>
  <outputs>
    <data format="tabular" name="bp1" label="${tool.name} on ${on_string}: Primary Breakpoints"/>
    <data format="tabular" name="bp2" label="${tool.name} on ${on_string}: Final Breakpoints"/>
    <data format="txt"	name="contigs" label="${tool.name} on ${on_string}: Contigs"/>
    <data format="txt" name="runlog" label="${tool.name} on ${on_string}: Runtime output"/>
  </outputs>
  <help>

**What it does**

ClusterFAST is a tool for finding translocation in next generation sequencing data developed by Haley Abel and Eric Duncavage at Washington University in St. Louis, MO. A manuscript detailing the use of ClusterFAST ican be found at: http://www.ncbi.nlm.nih.gov/pubmed/?term=24813172. For questions or comments please email [e-mail]

ClusterFAST is a pipeline for highly specific detection of translocations from high-coverage targeted capture sequence data. It detects translocation breakpoints with single base accuracy and provides assembled contigs for PCR validation. ClustFAST is implemented in Java for improved interoperability and can be run from the command line via a perl script. ClusterFAST is meant for translocation detection from targeted regions and requires a picard-style interval file containing the targets (e.g., ALK_MLL.txt). Numerous output files are created during the workflow (see below) to allow for error checking. The current version of ClusterFAST uses velvet to assemble contigs during the final step, however other assemblers can be substituted.  


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**Targets BED**

The BED file containing targets of interest. I would recommend to use one entry per gene of interest, instead of one entry per exon for this tool::

  Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1')
  Column 2: Start Position
  Column 3: End Position
  Column 4: Target Name.
  Column 5: Score : ignored, use '0'
  Column 6: Strand: ,'+' or '-'


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**Input formats**

BAM file for reads, BED file for targets.

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  </help>
</tool>