I am trying to make a simple tool that sends a command to run crimap 
without a wrapper ie.
crimap $param_file  $option  &gt;$output1

However, crimap expects a .par file as input (ie. $param_file should be a 
.par file). Because of this I get the error:
ERROR: Parameter file 
does not have '.par' suffix

Is there a simple way around this (using more lines in the command)? 
If I need to create a wrapper script, does somebody have an example that 
could help me to understand how it should be created? 
I am not familiar with python or perl and have written my other tools with 
R scripts embedded in the xml file ie.
        <command interpreter="sh">r_wrapper.sh $script_file</command>
                <configfile name="script_file">
etc etc

This is a similar issue.
This time I am trying to run another program called "crigen" without a 
wrapper as follows:
crigen -g $myData_gen -o $crimap_number -size $num_individ -gen $num_gen  
                <param name="label" type="text" value="name" size="30" 
label="short title for run"> </param>
                <param format="tabular" name="myData_gen" type="data" 
label="Choose .gen file" help="" > </param>
                <param name="crimap_number" type="integer" value="1" 
min="1" max="100000" label="number to identify output"> </param>
                <param name="num_individ" type="integer" value="50" 
min="1" max="10000" label="Number of individuals per family" help="limit 
of 1 to 10000"> </param>
                <param name="num_gen" type="integer" value="3" min="1" 
max="20" label="Number of generations" help="limit of 1 to 20"> </param>
                <data format="tabular" name="output1" label="crigen output 
 ${label}" />

In this case you need to use a number to identify the output in crigen. 
Running the tool is successful, but I get an empty output.

Appreciate any wrapper examples that deal with this sort of requirement 

Thanks and cheers, Nick
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