This was a first attempt at providing galaxy tool_wrappers for the Qiime metagenomics package:
You must first istall Qiime:  http://qiime.sourceforge.net/install/install.html



Initial tool wrappers were generated by a script searching the qiime scripts (version 1.2.1)  for usage info, 
and then were hand edited afterwards.  

NOTE:  A few of the tool configs worked on the galaxy-central code in April 2011.  
I haven't taken time to check them with more recent galaxy releases.


I executed the qiime scripts via qiime_wrapper.py
This was to accommmodate moving multiple outputs to history items:  http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files


The datatypes file:  metagenomics.py has Mothur datatypes with a start at qiime types added at the end.




The most common used qiime scripts are:
- check_id_map.py
- split_libraries.py
- pick_otus_through_otu_table.py
- beta_diversity_through_3d_plots.py
- alpha_rarefaction.py
- jackknifed_beta_diversity.py
- filter_by_metadata.py
- filter_otu_table.py
- merge_otu_tables.py
- merge_mapping_files.py


Tool_config development status:
The tool configs with a * indicate that the tool at least displayed in galaxy at least once upon time.
( Since these were intially auto generated, some may not make sense in a galaxy framework. )

	add_taxa.xml
	adjust_seq_orientation.xml
* 	align_seqs.xml		
*   	alpha_diversity.xml	metrics - select  input/output repeat   conditional tree
*	alpha_rarefaction.xml	
*	assign_taxonomy.xmlA	assignment_method-select
*	beta_diversity.xml 
*	beta_diversity_through_3d_plots.xml html-plots  
	beta_significance.xml
	blast_wrapper.xml
*	check_id_map.xml
	collate_alpha.xml
*	compare_3d_plots.xml
	consensus_tree.xml
	convert_otu_table_to_unifrac_sample_mapping.xml
	convert_unifrac_sample_mapping_to_otu_table.xml
*	denoise.xml
*	dissimilarity_mtx_stats.xml
	exclude_seqs_by_blast.xml
	extract_seqs_by_sample_id.xml
*	filter_alignment.xml
	filter_by_metadata.xml
	filter_fasta.xml
	filter_otu_table.xml
*	filter_otus_by_sample.xml
	fix_arb_fasta.xml
	identify_chimeric_seqs.xml
*	jackknifed_beta_diversity.xml
*	make_2d_plots.xml
*	make_3d_plots.xml
	make_bootstrapped_tree.xml
	make_distance_histograms.xml
	make_fastq.xml
	make_library_id_lists.xml
*	make_otu_heatmap_html.xml
*	make_otu_network.xml
	make_otu_table.xml
	make_per_library_sff.xml
	make_phylogeny.xml
	make_pie_charts.xml
	make_prefs_file.xml
	make_qiime_py_file.xml
*	make_qiime_rst_file.xml
*	make_rarefaction_plots.xml
*	make_sra_submission.xml
*	merge_denoiser_output.xml
	merge_mapping_files.xml
	merge_otu_maps.xml
	merge_otu_tables.xml
	multiple_rarefactions.xml
	multiple_rarefactions_even_depth.xml
	otu_category_significance.xml
*	parallel_align_seqs_pynast.xml
	parallel_alpha_diversity.xml
*	parallel_assign_taxonomy_blast.xml
*	parallel_assign_taxonomy_rdp.xml
	parallel_beta_diversity.xml
*	parallel_blast.xml
	parallel_identify_chimeric_seqs.xml
	parallel_multiple_rarefactions.xml
*	parallel_pick_otus_blast.xml
*	parallel_pick_otus_uclust_ref.xml
	per_library_stats.xml
*	pick_otus.xml
*	pick_otus_through_otu_table.xml
	pick_rep_set.xml
*	plot_rank_abundance_graph.xml
	poller.xml
	poller_example.xml
	pool_by_metadata.xml
	principal_coordinates.xml
	print_qiime_config.xml
*	process_sff.xml
*	process_sra_submission.xml
*	quality_scores_plot.xml
	shared_phylotypes.xml
	single_rarefaction.xml
	sort_denoiser_output.xml
*	split_libraries.xml
*	split_libraries_illumina.xml
	sra_spreadsheet_to_map_files.xml
	start_parallel_jobs.xml
	summarize_otu_by_cat.xml
	summarize_taxa.xml
*	supervised_learning.xml
*	transform_coordinate_matrices.xml
*	tree_compare.xml
	trflp_file_to_otu_table.xml
	trim_sff_primers.xml
*	truncate_fasta_qual_files.xml
	upgma_cluster.xml