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 <azuz...@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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