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 $option >$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 $num_gen
>$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___________________________________________________________
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