comparison mrbayes.xml @ 1:bd36a094f934 draft

planemo upload commit 5e6b76536ce524b849abf98220dcb1ec77570813-dirty

0:25da76152cf2

<?xml version="1.0"?>
<tool id="mrbayes" name="MrBayes" version="1.0.0">
  <description>with options and commands</description>
  <requirements>
    <requirement type="package" version="3.2.6">mrbayes</requirement>
  </requirements>
  <command> mb $command_file > $outfile
## print list of avaialble variables
#silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n")
#for k,v in $searchList[2].items()
#silent   sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))

#silent sys.stderr.write("======== End of Cheetah template variables ========\n \n \n")
  </command>
  <configfiles>
    <configfile name="command_file">
        begin mrbayes;
        set seed=$seed;
        set quitonerror=no;
        execute $data;
        outgroup $outgroup;
        $model;
        lset rates=$rates;

        help="Requires .ckp file (i.e. that number of generations > checkpoint frequency for previous analysis)." />
    <param name="seed" type="integer" label="&lt;hr&gt;Seed" optional="false" value="5"
      help="Specify a seed with which to run the job.">
      <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>
    </param>
  </inputs>
  <outputs>
    <data name="outfile" format="txt"/>
  </outputs>

1:bd36a094f934

<?xml version="1.0"?>
<tool id="mrbayes" name="MrBayes" version="1.0.1">
  <description>with options and commands</description>
  <requirements>
    <requirement type="package" version="3.2.6">mrbayes</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
  </stdio>
  <command> mb $command_file > $outfile
## print list of avaialble variables
#silent sys.stderr.write("\n \n \n ======== Cheetah template variables ========\n")
#for k,v in $searchList[2].items()
#silent   sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))

#silent sys.stderr.write("======== End of Cheetah template variables ========\n \n \n")
  </command>
  <configfiles>
    <configfile name="command_file">
        begin mrbayes;
        set Seed=$seed;
        set Swapseed=$swapseed;
        set quitonerror=no;
        execute $data;
        outgroup $outgroup;
        $model;
        lset rates=$rates;

        help="Requires .ckp file (i.e. that number of generations > checkpoint frequency for previous analysis)." />
    <param name="seed" type="integer" label="&lt;hr&gt;Seed" optional="false" value="5"
      help="Specify a seed with which to run the job.">
      <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>
    </param>
    <param name="swapseed" type="integer" label="&lt;hr&gt;Swap Seed" optional="false" value="5"
      help="Specify a swap seed with which to run the job.">
      <validator type="in_range" min="1" max="inf" message="Must be greater than or equal to 1"/>
    </param>
  </inputs>
  <outputs>
    <data name="outfile" format="txt"/>
  </outputs>