Hi VJ, you only can have one <command> tag in a tool, afaik. You can try to write it with cheetah and concatenate several shell commands with && or you can extend your python script to call your java tool at first step. Cheers, Bjoern

> input_file = sys.argv[1] > ... > txt_in = input_file + '.txt'

> output_file = sys.argv[2] > .. > pdf_out = output_file + '.pdf'

Apologies if my previous suggestion confused you : http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp... You may first generate the pdf : input_file = sys.argv[1] output_file = sys.argv[2] #txt_in = options.exp_data # + '.txt' ## NOT REQUIRED 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") pdf_out = output_file + '.pdf' plt.savefig(pdf_out) ## Write back to the output file ## You can do a shutil.move too [http://docs.python.org/2/library/shutil.html] ## like this : shutil.move(pdf_out,output_file)

data = file(output_file, 'rb').read()

fp = open(output_file, 'wb') fp.write(data) fp.close() I tried it locally and it worked. But this is under the assumptio that I am passing your python code the input-file from the Galaxy interface itself . I just created a CSV and ran the tool. The CSV was simple enough : 0 1 2 2 3 6 Saket On 11 July 2013 00:19, vijayalakshmi <vs49(a)buffalo.edu&gt; wrote: > Hi, > > I am trying to integrate a tool into galaxy. The tool runs in two parts - > 1) Computes correlation and provides an ouput 'txt' file (Java) 2) > Takes the previously ouput txt file and outputs a 'pdf' file. (Python) > > I am having trouble with the second tool. If I provide a sample 'txt' file > as input, it's working fine. But if I run it in galaxy, it is not working > (for some reason it is not reading the 'txt' file from the previous output). > Below is the code. > > > #!/usr/bin/python > > import sys, os > import numpy as np > import matplotlib.pyplot as plt > > input_file = sys.argv[1] > output_file = sys.argv[2] > > print 'Number of arguments:', len(sys.argv), 'arguments.' > print 'Argument List:', str(sys.argv) > > txt_in = input_file + '.txt' > mydata = np.loadtxt(txt_in) > 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") > pdf_out = output_file + '.pdf' > plt.savefig(pdf_out) > > data = file(pdf_out, 'rb').read() > fp = open(output_file, 'wb') > fp.write(data) > fp.close() > os.remove(txt_in) > os.remove(pdf_out) > > Below is the xml code. > > <tool id="archtex_massdata_extraction" name="Extract mass data"> > <description> for the given BAM file </description> > > <command> java -jar Extraction.jar > $input_bam_file $ref_filename $ref_filetype $output1 > </command> > <command interpreter="python"> plot.py $output1 $out_file1 > </command> > > <inputs> > <param name="input_bam_file" type="data" format="BAM" label="Input BAM file" > help="Choose an input BAM file"/> > <param name="ref_filename" type="data" format="gen,txt,gtf,bed" > label="Reference/Coordination file" help="Choose a reference file"/> > <param name="ref_filetype" type="select" label="Choose the reference file > type"> > <option value="custom">Custom</option> > <option value="refgene">refGene</option> > <option value="GFF">GFF</option> > <option value="bed">BED</option> > </param> > </inputs> > <outputs> > <data name="output1" format="txt" /> > <data name="out_file1" format="pdf" /> > </outputs> > </tool> > > I am forcing the input to be 'tx't and the output to be 'pdf' in the python > script. When I run the code, it is not showing any errors but it's not > showing any output either. I am able to download the first output 'txt' file > but there is no download button option in the right pane of galaxy for the > second part. > > Any help is appreciated! > > 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/