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