On 11 July 2013 04:31, Saket Choudhary <sake...@gmail.com> wrote:
> Apologies if my  previous suggestion confused you :
> http://dev.list.galaxyproject.org/error-while-writing-to-pdf-in-python-tp4660463p4660464.html
>
>
> 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()

Sorry the above line should be

      data = file(pdf_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 <v...@buffalo.edu> 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.
>>
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