Hi, I am writing a python script that will take in two parameters (an input file and an ouput file name) , plot a graph and output it to the filename specified. PYTHON SCRIPT #!/usr/bin/python import sys import numpy as np import matplotlib.pyplot as plt input_file = sys.argv[1] output_file = sys.argv[2] mydata = np.loadtxt(input_file) plt.figure(1) plt.plot(mydata[:,0],mydata[:,1],label = "Feature"); plt.plot(mydata[:,0],mydata[:,2], label = "Variance"); plt.xlabel('Distance from feature(bp)'); plt.ylabel('Score'); plt.title(sys.argv[1]); plt.legend(loc="best") plt.savefig(output_file) SAMPLE COMMAND : <command interpreter="python"> plot.py $ref_filename $out_file1 </command> <inputs> <param name="ref_filename" type="data" format="gen,txt,gtf,bed" label="Reference/Coordination file" help="Choose a reference file"/> </inputs> <outputs> <data name="out_file1" format="pdf" /> </outputs> When I run this, I am getting the following error. File "/panfs/panfs.ccr.buffalo.edu/projects/mjbuck/galaxy/CistromeAP/tools/ArchTex/plot.py", line 22, in <module> plt.savefig(output_file) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/pyplot.py", line 345, in savefig return fig.savefig(*args, **kwargs) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/figure.py", line 990, in savefig self.canvas.print_figure(*args, **kwargs) File "/data/apps/python/lib/python2.6/site-packages/matplotlib/backend_bases.py", line 1399, in print_figure '%s.' % (format, ', '.join(formats))) ValueError: Format "dat" is not supported. Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz. I don't know how to make the script extract ".pdf" from the ".dat" Thanks, VJ. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/