Rob,

I am not aware that there would be any issue, as I've verified all the
options with the Qiime documentation that is up now (and I've
eliminated those being deprecated).

Amanda Zuzolo

On 2/7/12, Jeffrey Long <jlo...@ualberta.ca> wrote:
> Hello Amanda,
> I was just about to embark on EXACTLY this process, so I would certainly be
> very interested in saving myself some work.
> Would there be any issue (that you're aware of, of course) with using QIIME
> 1.4.0 instead of 1.3?
>
> -Jeff
>
> On Tue, Feb 7, 2012 at 2:32 AM, Florent Angly
> <florent.an...@gmail.com>wrote:
>
>> Hi Amanda,
>> I would certainly be interested in using your helpful QIIME wrappers if
>> you put them on the Toolshed.
>> Best,
>> Florent
>>
>> On 06/02/12 06:22, Amanda Zuzolo wrote:
>>
>>> Hello, all.
>>>
>>> I have been working on getting the Qiime scripts into Galaxy as
>>> mentioned before, and they are working with Qiime 1.3.0. I have edited
>>> the wrapper file that Jim Johnson wrote to create more flexibility,
>>> especially in cases where the tool looks for a specific file type
>>> extension (for example, a .fna file), or where the tool normally
>>> outputs something to the command line that is not normally picked up
>>> in Galaxy.
>>>
>>> So far, I have completely finished fixing the XML files to the latest
>>> documentation for the entire Pick OTU process, Alpha Diversity, and
>>> Beta Diversity, as well as other miscellaneous functions. Currently, I
>>> am working on making scripts for jack-knifing functional. I determined
>>> that it would be easier to get individual scripts functional, rather
>>> than workflow scripts, since that allows the end-user to have more
>>> control. Additionally, the workflow scripts can easily be recreated by
>>> using Galaxy's workflows.
>>>
>>> As far as the toolshed goes, I don't believe I know the ins and outs
>>> yet, but I would be more than willing to learn if people would benefit
>>> from having these versions in that repository.
>>>
>>> 2012/1/29 Jim Johnson<johns...@umn.edu>:
>>>
>>>> Pat,
>>>>
>>>> That sounds great.   Do one of you want to take ownership of the
>>>> toolshed
>>>> repository?
>>>> At minimum, we should add developers to the list that can push changes.
>>>>
>>>> Thanks,
>>>>
>>>> JJ
>>>>
>>>> On 1/28/12 9:37 AM, Gillevet Patrick wrote:
>>>>
>>>> Jim et al
>>>>
>>>> Amanda has most of the scripts working now and will be putting them up
>>>> on
>>>> the toolshed.
>>>> She will be in touch as soon as the scripts are validated a couple of
>>>> times
>>>> with different datasets.
>>>>
>>>> cheers...
>>>> Pat
>>>>
>>>>
>>>>
>>>> On Dec 29, 2011, at 3:02 PM, Jim Johnson wrote:
>>>>
>>>>
>>>> It is easiest to generate tools for galaxy when the applications or
>>>> scripts
>>>> can take arbitrarily named input files and generate output to given
>>>> path
>>>> names.
>>>> Input directories, output directories are very convenient on the
>>>> command
>>>> line, but more of a challenge when crafting a galaxy tool.
>>>> That said, many applications require a wrapper script to work with in
>>>> galaxy.
>>>> Thank you for the consistent script_info[] help/usage syntax in the
>>>> qiime
>>>> scripts,  which enabled me to generate a skeleton galaxy tool_config
>>>> file
>>>> for each qiime script.
>>>>
>>>> I had some time last spring to work on integrating qiime into galaxy.
>>>> Unfortunately, I haven't had any time since to work on this.
>>>> I put those partial results  on the Galaxy Tool Shed:
>>>> http://toolshed.g2.bx.psu.edu/
>>>> There's a continuing effort at George Mason University to incorporate
>>>> qiime
>>>> into galaxy tools, so you may want to ask them what they need.
>>>>
>>>>
>>>> I started by generating galaxy tool_config files, e.g. align_seqs.xml,
>>>>  by
>>>> using python to get the script_info[] from the qiime script:
>>>>
>>>> $ cat generate_tool_config.bash
>>>> #!/usr/bin/env bash
>>>> python $1>  ${1%.*}.help
>>>> cat tool_template.txt | sed "s/__TOOL_BINARY__/${1}/" | python -i $1
>>>> -h>
>>>> ${1%.*}.log
>>>>
>>>> (I'll attach tool_template.txt )
>>>>
>>>> This generated skeleton tool_config .xml files that I could then edit
>>>> as
>>>> needed.
>>>> (
>>>> http://wiki.g2.bx.psu.edu/**Admin/Tools/Tool%20Config%**20Syntax<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax>)
>>>>
>>>> I originally was calling all qiime scripts from a tool wrapper:
>>>> qiime_wrapper.py
>>>> But, if a script can be called with any input filepaths and write its
>>>> results to any filepaths, and only writes to STDERR when it fails, then
>>>> you
>>>> could call that script directly.
>>>>
>>>>
>>>> When should you use a tool_wrapper or call the qiime script directly?
>>>>   Many of the qiime scripts could probably be called directly,
>>>> especially if
>>>> it can be called with arbitary input/output file pathnames.
>>>>   The reasons for using a tool wrapper may be if input/output needs to
>>>> be
>>>> manipulated, moved, renamed in order to be used by the qiime script.
>>>>   You'll also need a tool wrapper if the names or number of the output
>>>> files
>>>> can not be determined from the parameter settings.
>>>>   (
>>>> http://wiki.g2.bx.psu.edu/**Admin/Tools/Multiple%20Output%**20Files<http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files>)
>>>>   If your tool relies on a file ext to determine a format, you'll have
>>>> to
>>>> rename the input.
>>>>   ( Galaxy dataset pathnames will look something like:
>>>> /<your_galaxy_file_path>/072/**dataset_72931.dat )
>>>>   The format/type of a dataset is stored in its metadata, so the
>>>> tool_config
>>>> can use that information, especially if a script can take muliple
>>>> alternative input formats.
>>>>   A tool_wrapper can also be used to manage the stdout or stderr from a
>>>> tool.   Galaxy currently interprets any output on stderr as a failure.
>>>>
>>>>
>>>>
>>>> A couple changes in galaxy should make somethings easier than when I
>>>> first
>>>> attempted this:
>>>>   - galaxy now accepts dataset requests with sub directories. (
>>>> https://bitbucket.org/galaxy/**galaxy-central/issue/494/**
>>>> support-sub-dirs-in-extra_**files_path-patch<https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch>
>>>> )
>>>>     That means that output HTML files with links into sub directories
>>>> can be
>>>> left intact, with the html copied to the output dataset and the linked
>>>> files
>>>> to its "extra_files_path".
>>>>   - if you know the pathname of an output relative to the working
>>>> directory,
>>>> galaxy can copy it automatically to the output dataset using the
>>>> from_work_dir attribute.
>>>>     ( see example in:
>>>> https://bitbucket.org/galaxy/**galaxy-central/src/**
>>>> 21b645303c02/tools/ngs_rna/**tophat_wrapper.xml<https://bitbucket.org/galaxy/galaxy-central/src/21b645303c02/tools/ngs_rna/tophat_wrapper.xml>
>>>> )
>>>>
>>>> Datatypes
>>>>   You may want to create new datatypes to make it easier for the user
>>>> to
>>>> correctly select inputs to a tool from previous outputs.
>>>>   For example, the qiime mapping file is a tabular file with specific
>>>> requirements.  I put a 'qiimemapping' datatype in
>>>> lib/galaxy/datatypes/**metagenomics.py and datatypes_conf.xml
>>>>   so an input could generate a select list containing only qiimemapping
>>>> datasets rather than all tabular ones.
>>>>
>>>> Generating a configfile
>>>>   You can generate configfiles in the galaxy tool_config .xml file.
>>>> The
>>>> configfile is generated by the Cheetah interpreter just as the
>>>> commandline
>>>> is.
>>>>   see:  alpha_rarefaction.xml
>>>>
>>>> The qiime_wrapper.py was patterned after the mothur_wrapper.py   with
>>>> some
>>>> of the same wrapper params to handle run time determined output
>>>> (perhaps
>>>> not
>>>> needed):
>>>>   --galaxy_datasets
>>>>          a comma separated list of regex:output_dataset the wrapper
>>>> searches
>>>> the working_dir and copies the file that matches the regex to the
>>>> outout
>>>> dataset
>>>>          if the exact pathname is known, use the "from_work_dir"
>>>> attribute
>>>> instead
>>>>   --galaxy_datasetid
>>>>          would be an output dataset id that would be used to
>>>> dynamically
>>>> create additional new datasets at job termination
>>>>          ( http://wiki.g2.bx.psu.edu/**Admin/Tools/Multiple%20Output%**
>>>> 20Files<http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files>
>>>> "Number of Output datasets cannot be determined until tool run")
>>>>   --galaxy_new_datasets
>>>>          a comma separated list of regex:datatype used to dynamically
>>>> create
>>>> additional new datasets at job termination
>>>>   --galaxy_new_files_path
>>>>          the galaxy dir for dynamically generated output datasets
>>>>
>>>>
>>>>
>>>>
>>>> ****************************************************************
>>>> *****************************
>>>>                                 Patrick M. Gillevet, Ph.D.
>>>>                        Director, Microbiome Analysis Center
>>>>     Professor, Department of Environmental Science and Policy
>>>>                Affiliate Professor, School of Systems Biology
>>>>              George Mason University, Prince William Campus
>>>>                     10900 University Boulevard, MSN 4D4
>>>>                              Manassas, Virginia  20110
>>>>
>>>> Office 703-993-1057     Room Occoquan-426     FAX 703-993-8430
>>>>                                       http://mbac.gmu.edu
>>>> ****************************************************************
>>>> ******************************
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
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