here's what i have; i started categorizing the tools under labels but hadn't finished. i'm also working on getting these tools working in galaxy (albeit slowly as we won't need them until we get a miseq machine in oct), but maybe we can be in communication with each other and jjohnson.

<section name="QIIME (testing; under development)" id="qiime_tools">

<label text="UNDER DEVELOPMENT" id="QIIME_TESTING"/>

<label text="Preprocessing/QC" id="qiime_preprocessing"/>

<tool file="qiime/check_id_map.xml" />

<tool file="qiime/split_libraries.xml" />

<tool file="qiime/denoise.xml" />

<tool file="qiime/sort_denoiser_output.xml" />

<tool file="qiime/trim_sff_primers.xml" />

<tool file="qiime/fix_arb_fasta.xml" />

<tool file="qiime/quality_scores_plot.xml" />

<tool file="qiime/truncate_fasta_qual_files.xml" />

<tool file="qiime/process_sff.xml" />

<tool file="qiime/identify_chimeric_seqs.xml" />

<tool file="qiime/parallel_identify_chimeric_seqs.xml" />

<tool file="qiime/split_libraries_illumina.xml" />

<tool file="qiime/make_library_id_lists.xml" />

<tool file="qiime/make_fastq.xml" />

<tool file="qiime/merge_denoiser_output.xml" />

<tool file="qiime/adjust_seq_orientation.xml" />

<tool file="qiime/extract_seqs_by_sample_id.xml" />

<label text="Pick OTUs" id="qiime_otus"/>

<tool file="qiime/parallel_pick_otus_blast.xml" />

<tool file="qiime/pick_otus_through_otu_table.xml" />

<tool file="qiime/parallel_pick_otus_uclust_ref.xml" />

<tool file="qiime/pick_rep_set.xml" />

<tool file="qiime/parallel_assign_taxonomy_rdp.xml" />

<tool file="qiime/parallel_assign_taxonomy_blast.xml" />

<tool file="qiime/make_phylogeny.xml" />

<tool file="qiime/make_otu_table.xml" />

<tool file="qiime/pick_otus.xml" />

<tool file="qiime/filter_alignment.xml" />

<label text="Align OTUs" id="qiime_align"/>

<tool file="qiime/parallel_align_seqs_pynast.xml" />

<tool file="qiime/blast_wrapper.xml" />

<tool file="qiime/parallel_blast.xml" />

<tool file="qiime/exclude_seqs_by_blast.xml" />

<tool file="qiime/align_seqs.xml" />

<label text="OTU Analysis" id="qiime_otu_analysis"/>

<tool file="qiime/assign_taxonomy.xml" />

<tool file="qiime/per_library_stats.xml" />

<tool file="qiime/make_otu_heatmap_html.xml" />

<tool file="qiime/make_otu_network.xml" />

<tool file="qiime/summarize_taxa.xml" />

<tool file="qiime/filter_otu_table.xml" />

<label text="Diversity Analysis" id="qiime_diversity"/>

<tool file="qiime/multiple_rarefactions.xml" />

<tool file="qiime/multiple_rarefactions_even_depth.xml" />

<tool file="qiime/parallel_multiple_rarefactions.xml" />

<tool file="qiime/alpha_diversity.xml" />

<tool file="qiime/alpha_rarefaction.xml" />

<tool file="qiime/parallel_alpha_diversity.xml" />

<tool file="qiime/collate_alpha.xml" />

<tool file="qiime/make_rarefaction_plots.xml" />

<tool file="qiime/single_rarefaction.xml" />

<tool file="qiime/beta_diversity.xml" />

<tool file="qiime/beta_diversity_through_3d_plots.xml" />

<tool file="qiime/compare_3d_plots.xml" />

<tool file="qiime/beta_significance.xml" />

<tool file="qiime/jackknifed_beta_diversity.xml" />

<tool file="qiime/parallel_beta_diversity.xml" />

<tool file="qiime/make_prefs_file.xml" />

<tool file="qiime/principal_coordinates.xml" />

<tool file="qiime/make_2d_plots.xml" />

<tool file="qiime/make_3d_plots.xml" />

<tool file="qiime/make_distance_histograms.xml" />

<tool file="qiime/upgma_cluster.xml" />

<tool file="qiime/tree_compare.xml" />

<tool file="qiime/consensus_tree.xml" />

<label text="More" id="qiime_more"/>

<tool file="qiime/poller_example.xml" />

<tool file="qiime/filter_fasta.xml" />

<tool file="qiime/add_taxa.xml" />

<tool file="qiime/make_qiime_rst_file.xml" />

<tool file="qiime/otu_category_significance.xml" />

<tool file="qiime/poller.xml" />

<tool file="qiime/supervised_learning.xml" />

<tool file="qiime/merge_mapping_files.xml" />

<tool file="qiime/dissimilarity_mtx_stats.xml" />

<tool file="qiime/summarize_otu_by_cat.xml" />

<tool file="qiime/transform_coordinate_matrices.xml" />

<tool file="qiime/merge_otu_maps.xml" />

<tool file="qiime/start_parallel_jobs.xml" />

<tool file="qiime/plot_rank_abundance_graph.xml" />

<tool file="qiime/sort_otu_table.xml" />

<tool file="qiime/make_bootstrapped_tree.xml" />

<tool file="qiime/trflp_file_to_otu_table.xml" />

<tool file="qiime/pool_by_metadata.xml" />

<tool file="qiime/submit_to_mgrast.xml" />

<tool file="qiime/pick_reference_otus_through_otu_table.xml" />

<tool file="qiime/merge_otu_tables.xml" />

<tool file="qiime/filter_by_metadata.xml" />

<tool file="qiime/plot_taxa_summary.xml" />

<tool file="qiime/make_per_library_sff.xml" />

<tool file="qiime/convert_unifrac_sample_mapping_to_otu_table.xml" />

<tool file="qiime/categorized_dist_scatterplot.xml" />

<tool file="qiime/shared_phylotypes.xml" />

<tool file="qiime/print_qiime_config.xml" />

<tool file="qiime/convert_otu_table_to_unifrac_sample_mapping.xml" />

<tool file="qiime/make_qiime_py_file.xml" />

<tool file="qiime/make_pie_charts.xml" />

<tool file="qiime/filter_otus_by_sample.xml" />

</section>

On Wed, Jul 27, 2011 at 7:01 AM, Amanda Zuzolo <azuzolo@gmu.edu> wrote:

Hello all,

I'm working on a local instance of Galaxy at George Mason University. We'd been looking into integrating Qiime and I've found the toolkit very helpful, thanks! I did have one question, though: would you mind uploading the tool_conf file or chunk of text with the qiime functions in it? This would be helpful to myself, as well as others interested in the toolkit!

Thank you,

Amanda Zuzolo
Bioengineering Major, George Mason University

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