comparison README @ 0:e5c3175506b7 default tip

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:
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,
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.
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
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:
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
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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