comparison defuse.xml @ 12:4fe2e80d4ae1 draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 0eb27e6896eacbb49a979fa4b34c31859e7fb1a8-dirty

11:b22f8634ff84

        <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
      -->
      <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
    </when> <!-- full -->
  </conditional>  <!-- defuse_param -->
  <param name="breakpoints_bam" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
  <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
         help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
               but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
 </inputs>
 <stdio>
   <exit_code range="1:"  level="fatal" description="Error Running Defuse" />
 </stdio>

12:4fe2e80d4ae1

        <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
      -->
      <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
    </when> <!-- full -->
  </conditional>  <!-- defuse_param -->
  <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
         help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
               but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
  <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
 </inputs>
 <stdio>
   <exit_code range="1:"  level="fatal" description="Error Running Defuse" />
 </stdio>