Hi,

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

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 '/home/galaxy/galaxy-dist/database/job_working_directory/001/1434/tmpe5hErw' 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>
        <configfiles>
                <configfile name="script_file">
etc etc
                </configfile>
        </configfiles>

2. OUTPUT
This is a similar issue.
This time I am trying to run another program called "crigen" without a wrapper as follows:
................
        <command>
crigen -g $myData_gen -o $crimap_number -size $num_individ -gen $num_gen  &gt;$output1
</command>
        <inputs>
                <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>
        </inputs>
        <outputs>
                <data format="tabular" name="output1" label="crigen output  ${label}" />
        </outputs>

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 too.

Thanks and cheers, Nick