HI Vijayalakshmi, You can take tools/plotting/plotter.py as an example : See line 81 : png_out = out_file + '.png' # force it to png So in your case : You can force it to pdf : output_file = sys.argv[2] +".pdf" I think this should work. Saket On 2 July 2013 23:37, vijayalakshmi <vs49@buffalo.edu> wrote:

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.

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