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

> 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/



___________________________________________________________
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/

Reply via email to