[galaxy-dev] Tool availability

Hi, Are any of the following tools available in galaxy? 1) IDRhttp://www.uwencode.org/software/hotspot 2) Hotspot https://sites.google.com/site/anshulkundaje/projects/idr 3) Wiggler https://code.google.com/p/align2rawsignal/ 4) PhantomPeakQualTools Regards, Vijayalakshmi

[galaxy-dev] problem with python output

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'

[galaxy-dev] error while writing to pdf in python

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

[galaxy-dev] displaying further input based on previous input

Hi all, I am trying to format the input to a java tool that I am writing. I want to display different options to choose from based on the user input. I am not sure how to do that. For example, based on the input file, I want to display the chromosome options to choose from. How do I do this?

[galaxy-dev] setting parameters for uploading a file for a java program

Hi all, I have a tool written in java for which I want to upload a file as a parameter. I have trouble figuring out how to do it. I tried writing the xml file similar to 'tools/data-source/upload.xml' but it is not working. *correlation.xml* tool id=correlation name=Compute correlation

[galaxy-dev] displaying further input based on previous input

Hi all, I am trying to format the input to a java tool that I am writing. I want to display different options to choose from based on the user input. I am not sure how to do that. For example, based on the input file, I want to display the chromosome options to choose from. How do I do this?

Re: [galaxy-dev] problem integrating new jar file

Hi, I am trying to integrate a tool that is written in java into galaxy. The following is what I've done. 1) Created a directory inside /tools directory and put my xml and runnable jar file in it. 2) Linked the xml file in 'tool_conf.xml'. *tool_conf.xml* section name=sample

[galaxy-dev] formatting output from a java tool

Hi all, I am trying to integrate a tool written in java into galaxy. The tool opens a GUI window to output a graph and also writes a text file. I want to know how to output that graph in the middle pane and how to output the text file so that the user will be able to download it.

[galaxy-dev] printing output from java tool in the middle pane in galaxy

Hi all, I am trying to integrate a tool written in java into galaxy. The java code will output a GUI window. I want to know how to output that window in the middle pane Thanks, VJ ___ Please keep all replies on the list by using reply

[galaxy-dev] problem integrating new jar file

Hi, I am trying to integrate a tool that is written in java into galaxy. The following is what I've done. 1) Created a directory inside /tools directory and put my xml and runnable jar file in it. 2) Linked the xml file in 'tool_conf.xml'. *tool_conf.xml* section name=sample tool

[galaxy-dev] XML files for MACS v1.4

HI all, I am trying to integrate MACS v1.4 into Galaxy. But I am unable to find the XML for the following MACS tools 1) elandexport2bed 2) elandmulti2bed 3) elandresult2bed 4) macs14 5) sam2bed 6) wignorm Any pointer/guidance is appreciated. Thanks, VJ.

[galaxy-dev] command tag in xml file for a C++ tool

Hi all, I want to include a new tool to galaxy. The tool is written in C++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate ishttps://code.google.com/p/bedtools/ I have the class file to be executed and the command to execute it. For example,

[galaxy-dev] writing command tag in xml file for a C++ tool

Hi all, I want to include a new tool to galaxy. The tool is written in C++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate ishttps://code.google.com/p/bedtools/ I have the class file to be executed and the command to execute it. For example,

[galaxy-dev] changing the order of display in the left pane

Hi all, I am trying to deploy Galaxy in my local server with some modifications. But when I change the order of section inside toolbox in *tool_conf.xml * file , it's NOT taking effect. Should I modify some other files to change the order of display in the left pane?? Thanks, VJ.

[galaxy-dev] finding parts of tool_conf.xml

Hi all, I am trying to get the *tool_conf.xml* section code corresponding to the following topics listed below. I am unable to find it in both the default build and the stable build in bitbucket. If you can point me to where I can find it, it'd be swell. 1) NGS: Variant detection 2) NGS:

[galaxy-dev] changing the order of display in the left pane

Hi all, I am trying to deploy Galaxy in my local server with some modifications. But when I change the order of section inside toolbox in *tool_conf.xml * file , it's NOT taking effect. Should I modify some other files to change the order of display in the left pane?? Thanks, VJ.

[galaxy-dev] finding parts of tool_conf.xml

Hi all, I am trying to get the *tool_conf.xml* section code corresponding to the following topics listed below. I am unable to find it in both the default build and the stable build in bitbucket. If you can point me to where I can find it, it'd be swell. 1) NGS: Variant detection 2) NGS: