annotate gaussian.xml @ 2:ed472dc06c20 draft default tip

Uploaded 1.0.0

<tool id="gaussian" name="Gaussian" version="1.0.0">
<!--
Copyright (C) 2012
Ying Zhang <[e-mail]> and Oleksandr Moskalenko <[e-mail]>
University of Florida Research Computing
-->
  <description>Computational Chemistry software for electronic structure modeling.</description>
  <command interpreter="python">gaussian.py $__user_name__ $infile</command>
  <inputs>
        <param format="txt" name="infile" type="data" label="Gaussian Input File"/>
  </inputs>
  <outputs>
        <data format="txt" name="outfile" type="data" from_work_dir="gaussian.log" label="${tool.name} on ${on_string}: Output" />
  </outputs>
  <!--
  <stdio>
        <exit_code range="1:"   level="fatal"   description="Tool Error - see debug log." />
        <exit_code range="2:"   level="fatal"   description="Unauthorized user - see help." />
  </stdio>
  -->
  <tests>
    <test>
      <param name="infile" value="chemistry/gaussian/gaussian.com"/>
      <output name="outfile" file="chemistry/gaussian/gaussian.log"/>
    </test>
</tests>

  <help>
**Gaussian version g09**

Gaussian is Electronic Structure Modeling Software. It has license restrictions.
To run it you must sign the Gaussian Confidentiality Agreement. The agreement
form is available in NPB 2238 during normal business hours.


Running Gaussian from Galaxy is currently in testing stage. Please report any
problems to the `UF HPC Support &lt;http://support.hpc.ufl.edu&gt;`_.


Batch job resource request can be specified at the beginning of the input file
as in the following example:

&#37;nproc=8 - number of cores (ppn).

&#37;mem=2000mb - memory size (pmem) can be set in kb, mb, gb, kw, mw, or gw. Words are used as the default.

!walltime=12:00:00 - run time (walltime) in HH:MM:SS format.


Detailed information on program usage is available from `the Gaussian website &lt;http://www.gaussian.com/&gt;`_.
  </help>
</tool>