Mercurial > repos > jjohnson > qiime
comparison README @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 This was a first attempt at providing galaxy tool_wrappers for the Qiime metagenomics package: | |
| 2 You must first istall Qiime: http://qiime.sourceforge.net/install/install.html | |
| 3 | |
| 4 | |
| 5 | |
| 6 Initial tool wrappers were generated by a script searching the qiime scripts (version 1.2.1) for usage info, | |
| 7 and then were hand edited afterwards. | |
| 8 | |
| 9 NOTE: A few of the tool configs worked on the galaxy-central code in April 2011. | |
| 10 I haven't taken time to check them with more recent galaxy releases. | |
| 11 | |
| 12 | |
| 13 I executed the qiime scripts via qiime_wrapper.py | |
| 14 This was to accommmodate moving multiple outputs to history items: http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files | |
| 15 | |
| 16 | |
| 17 The datatypes file: metagenomics.py has Mothur datatypes with a start at qiime types added at the end. | |
| 18 | |
| 19 | |
| 20 | |
| 21 | |
| 22 The most common used qiime scripts are: | |
| 23 - check_id_map.py | |
| 24 - split_libraries.py | |
| 25 - pick_otus_through_otu_table.py | |
| 26 - beta_diversity_through_3d_plots.py | |
| 27 - alpha_rarefaction.py | |
| 28 - jackknifed_beta_diversity.py | |
| 29 - filter_by_metadata.py | |
| 30 - filter_otu_table.py | |
| 31 - merge_otu_tables.py | |
| 32 - merge_mapping_files.py | |
| 33 | |
| 34 | |
| 35 Tool_config development status: | |
| 36 The tool configs with a * indicate that the tool at least displayed in galaxy at least once upon time. | |
| 37 ( Since these were intially auto generated, some may not make sense in a galaxy framework. ) | |
| 38 | |
| 39 add_taxa.xml | |
| 40 adjust_seq_orientation.xml | |
| 41 * align_seqs.xml | |
| 42 * alpha_diversity.xml metrics - select input/output repeat conditional tree | |
| 43 * alpha_rarefaction.xml | |
| 44 * assign_taxonomy.xmlA assignment_method-select | |
| 45 * beta_diversity.xml | |
| 46 * beta_diversity_through_3d_plots.xml html-plots | |
| 47 beta_significance.xml | |
| 48 blast_wrapper.xml | |
| 49 * check_id_map.xml | |
| 50 collate_alpha.xml | |
| 51 * compare_3d_plots.xml | |
| 52 consensus_tree.xml | |
| 53 convert_otu_table_to_unifrac_sample_mapping.xml | |
| 54 convert_unifrac_sample_mapping_to_otu_table.xml | |
| 55 * denoise.xml | |
| 56 * dissimilarity_mtx_stats.xml | |
| 57 exclude_seqs_by_blast.xml | |
| 58 extract_seqs_by_sample_id.xml | |
| 59 * filter_alignment.xml | |
| 60 filter_by_metadata.xml | |
| 61 filter_fasta.xml | |
| 62 filter_otu_table.xml | |
| 63 * filter_otus_by_sample.xml | |
| 64 fix_arb_fasta.xml | |
| 65 identify_chimeric_seqs.xml | |
| 66 * jackknifed_beta_diversity.xml | |
| 67 * make_2d_plots.xml | |
| 68 * make_3d_plots.xml | |
| 69 make_bootstrapped_tree.xml | |
| 70 make_distance_histograms.xml | |
| 71 make_fastq.xml | |
| 72 make_library_id_lists.xml | |
| 73 * make_otu_heatmap_html.xml | |
| 74 * make_otu_network.xml | |
| 75 make_otu_table.xml | |
| 76 make_per_library_sff.xml | |
| 77 make_phylogeny.xml | |
| 78 make_pie_charts.xml | |
| 79 make_prefs_file.xml | |
| 80 make_qiime_py_file.xml | |
| 81 * make_qiime_rst_file.xml | |
| 82 * make_rarefaction_plots.xml | |
| 83 * make_sra_submission.xml | |
| 84 * merge_denoiser_output.xml | |
| 85 merge_mapping_files.xml | |
| 86 merge_otu_maps.xml | |
| 87 merge_otu_tables.xml | |
| 88 multiple_rarefactions.xml | |
| 89 multiple_rarefactions_even_depth.xml | |
| 90 otu_category_significance.xml | |
| 91 * parallel_align_seqs_pynast.xml | |
| 92 parallel_alpha_diversity.xml | |
| 93 * parallel_assign_taxonomy_blast.xml | |
| 94 * parallel_assign_taxonomy_rdp.xml | |
| 95 parallel_beta_diversity.xml | |
| 96 * parallel_blast.xml | |
| 97 parallel_identify_chimeric_seqs.xml | |
| 98 parallel_multiple_rarefactions.xml | |
| 99 * parallel_pick_otus_blast.xml | |
| 100 * parallel_pick_otus_uclust_ref.xml | |
| 101 per_library_stats.xml | |
| 102 * pick_otus.xml | |
| 103 * pick_otus_through_otu_table.xml | |
| 104 pick_rep_set.xml | |
| 105 * plot_rank_abundance_graph.xml | |
| 106 poller.xml | |
| 107 poller_example.xml | |
| 108 pool_by_metadata.xml | |
| 109 principal_coordinates.xml | |
| 110 print_qiime_config.xml | |
| 111 * process_sff.xml | |
| 112 * process_sra_submission.xml | |
| 113 * quality_scores_plot.xml | |
| 114 shared_phylotypes.xml | |
| 115 single_rarefaction.xml | |
| 116 sort_denoiser_output.xml | |
| 117 * split_libraries.xml | |
| 118 * split_libraries_illumina.xml | |
| 119 sra_spreadsheet_to_map_files.xml | |
| 120 start_parallel_jobs.xml | |
| 121 summarize_otu_by_cat.xml | |
| 122 summarize_taxa.xml | |
| 123 * supervised_learning.xml | |
| 124 * transform_coordinate_matrices.xml | |
| 125 * tree_compare.xml | |
| 126 trflp_file_to_otu_table.xml | |
| 127 trim_sff_primers.xml | |
| 128 * truncate_fasta_qual_files.xml | |
| 129 upgma_cluster.xml |