--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,129 @@
+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