comparison somatic_sniper.xml @ 2:f7d69881bdec draft default tip

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1:2ff18e84c946

  #end if

	
  ## BUILD SOMATICSNIPER COMMAND LINE 
  \$CONDA_DEFAULT_ENV/bin/bam-somaticsniper
    -F vcf
    -q $advancedsettings.q
    -Q $advancedsettings.Q
    -T $advancedsettings.T
    -N $advancedsettings.N

				<option value="cached" selected="True">Use a built-in genome</option>
				<option value="history">Use a genome from the history</option>
			</param>
			<when value="cached">
				<param name="index" type="select" label="Reference Genome File" >
					<options from_data_table="all_fasta" />
				</param>
      			</when>
      			<when value="history">
        			<param format="fasta" name="ownFile" type="data" metadata_name="dbkey" label="Reference Genome File" />
      			</when>

                  <output name="variants" file="sniper_results.vcf" />
                </test>
        </tests>
	<help>
		http://gmt.genome.wustl.edu/packages/somatic-sniper/
	</help>
</tool>

2:f7d69881bdec

  #end if

	
  ## BUILD SOMATICSNIPER COMMAND LINE 
  bam-somaticsniper
    -F vcf
    -q $advancedsettings.q
    -Q $advancedsettings.Q
    -T $advancedsettings.T
    -N $advancedsettings.N

				<option value="cached" selected="True">Use a built-in genome</option>
				<option value="history">Use a genome from the history</option>
			</param>
			<when value="cached">
				<param name="index" type="select" label="Reference Genome File" >
					<options from_data_table="sniper_index" />
				</param>
      			</when>
      			<when value="history">
        			<param format="fasta" name="ownFile" type="data" metadata_name="dbkey" label="Reference Genome File" />
      			</when>

                  <output name="variants" file="sniper_results.vcf" />
                </test>
        </tests>
	<help>
		http://gmt.genome.wustl.edu/packages/somatic-sniper/

this wrapper was developed from https://github.com/morinlab/tools-morinlab/tree/master/tools/somatic_sniper only the requirement and part of the command line have been changed in order to make it suitable for CONDA

	</help>
</tool>