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.angly@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<johns198@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 )

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 )
  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
)
    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
)

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
"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




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