Provide tool usage statistics

[hechth]

It would be great if it would be possible to provide tool usage statistics - either via some visualizations (similar to stats.galaxyproject.eu) or via a table, similar to the files provided for the galaxy_codex (here). This would be super useful for reporting and for the communities as well if this would be added to the galaxy_codex. Maybe we could setup a CI action which will update the table and open a PR every month or so?

[martindemko]

Hi, sure, some reporting could and should be arranged. The question is if you need it ASAP in any simple form (like table in galaxy_codex), or if you prefer to have own Grafana deployed (which will take more time). Both options are valid and doable.

[martenson]

@martindemko let's do a basic report via gxadmin database query now, and worry about more advanced solution later

[martindemko]

Here you have a table from today, the CI action is a great idea, but first we need to merge UMSA playbook with our new standard.

toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2                                                                    | 27127
Cut1                                                                                                                                              | 21279
testing_pbs                                                                                                                                       | 16408
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toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/0.13.4+galaxy0                   |  2548
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_remove_noise/recetox_aplcms_remove_noise/0.13.4+galaxy0                                       |  2548
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_remove_noise/recetox_aplcms_remove_noise/0.13.3+galaxy0                                       |  1489
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/0.13.3+galaxy0                   |  1488
toolshed.g2.bx.psu.edu/repos/recetox/target_screen/target_screen/0.1.0+galaxy0                                                                    |  1213
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_correct_time/recetox_aplcms_correct_time/0.13.3+galaxy0                                       |  1149
__ZIP_COLLECTION__                                                                                                                                |   810
toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy3                                                     |   717
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy3                                                           |   712
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1                                                                |   350
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_remove_noise/recetox_aplcms_remove_noise/0.12.0+galaxy3                                       |   201
Grep1                                                                                                                                             |   175
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1                                                               |   173
CONVERTER_parquet_to_csv                                                                                                                          |   169
csv_to_tabular                                                                                                                                    |   159
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0                                                                                   |   159
__DATA_FETCH__                                                                                                                                    |   118
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1                                                           |    88
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toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_remove_noise/recetox_aplcms_remove_noise/0.13.2+galaxy0                                       |    62
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toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_generate_feature_table/recetox_aplcms_generate_feature_table/0.13.2+galaxy0                   |    62
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_correct_time/recetox_aplcms_correct_time/0.13.2+galaxy0                                       |    62
cat1                                                                                                                                              |    61
toolshed.g2.bx.psu.edu/repos/recetox/assign_ri_from_comment/riassigner_from_comment/0.4.1+galaxy0                                                 |    50
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_clusters/recetox_aplcms_compute_clusters/0.13.3+galaxy0                               |    42
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/0.13.4+galaxy0                                   |    40
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_clusters/recetox_aplcms_compute_clusters/0.13.4+galaxy0                               |    39
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.8+galaxy0                                                                               |    35
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/0.13.3+galaxy0                                   |    33
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_template/recetox_aplcms_compute_template/0.13.3+galaxy0                               |    25
__DUPLICATE_FILE_TO_COLLECTION__                                                                                                                  |    25
__CROSS_PRODUCT_FLAT__                                                                                                                            |    21
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2                                                    |    19
toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.3.0+galaxy7                                                                            |    18
__APPLY_RULES__                                                                                                                                   |    15
toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy2                                                     |    14
__EXTRACT_DATASET__                                                                                                                               |    14
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toolshed.g2.bx.psu.edu/repos/recetox/waveica/waveica/0.2.0+galaxy8                                                                                |    13
toolshed.g2.bx.psu.edu/repos/recetox/matchms_convert/matchms_convert/0.27.0+galaxy0                                                               |    12
toolshed.g2.bx.psu.edu/repos/recetox/matchms_filtering/matchms_filtering/0.27.0+galaxy0                                                           |    12
tabular_to_csv                                                                                                                                    |    11
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toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_recover_weaker_signals/recetox_aplcms_recover_weaker_signals/0.12.0+galaxy3                   |    10
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_correct_time/recetox_aplcms_correct_time/0.12.0+galaxy3                                       |    10
toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata/msnbase_readmsdata/2.16.1+galaxy0                                                     |     9
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toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy0                                                           |     9
toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.25.0+galaxy0                                                           |     9
__MERGE_COLLECTION__                                                                                                                              |     8
toolshed.g2.bx.psu.edu/repos/recetox/matchms_spectral_similarity/matchms_spectral_similarity/0.25.0+galaxy0                                       |     8
toolshed.g2.bx.psu.edu/repos/recetox/matchms_metadata_export/matchms_metadata_export/0.27.0+galaxy0                                               |     7
toolshed.g2.bx.psu.edu/repos/recetox/recetox_msfinder/recetox_msfinder/v3.5.2+galaxy4                                                             |     7
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy3                                                                     |     7
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy3                                                               |     7
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_clusters/recetox_aplcms_compute_clusters/0.12.0+galaxy3                               |     7
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/abims_xcms_summary/3.12.0+galaxy3                                                           |     6
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy3                                                       |     6
__FILTER_FROM_FILE__                                                                                                                              |     6
toolshed.g2.bx.psu.edu/repos/recetox/ms2deepscore_training/ms2deepscore_training/2.0.0+galaxy0                                                    |     5
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_kmdnoise/mfassignr_kmdnoise/1.1.2+galaxy0                                                          |     5
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassign/mfassignr_mfassign/1.1.2+galaxy1                                                          |     5
toolshed.g2.bx.psu.edu/repos/recetox/rcx_tk/rcx-tk/0.1.0+galaxy0                                                                                  |     5
toolshed.g2.bx.psu.edu/repos/recetox/msmetaenhancer/msmetaenhancer/0.4.0+galaxy1                                                                  |     5
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy3                                     |     5
toolshed.g2.bx.psu.edu/repos/recetox/matchms_metadata_match/matchms_metadata_match/0.25.0+galaxy0                                                 |     5
toolshed.g2.bx.psu.edu/repos/recetox/rename_annotated_feature/rename_annotated_feature/1.0.0+galaxy0                                              |     5
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/0.12.0+galaxy2                                   |     4
toolshed.g2.bx.psu.edu/repos/recetox/riassigner/riassigner/0.4.1+galaxy0                                                                          |     4
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_isofiltr/mfassignr_isofiltr/1.1.2+galaxy1                                                          |     4
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_findrecalseries/mfassignr_findRecalSeries/1.1.1+galaxy0                                            |     3
__BUILD_LIST__                                                                                                                                    |     3
__FLATTEN__                                                                                                                                       |     3
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy3                                                             |     3
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy1                                                           |     3
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassigncho/mfassignr_mfassignCHO/1.1.2+galaxy1                                                    |     3
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_recal/mfassignr_recal/1.1.2+galaxy0                                                                |     3
toolshed.g2.bx.psu.edu/repos/recetox/ms2deepscore_config_generator/ms2deepscore_config_generator/2.0.0+galaxy0                                    |     3
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_clusters/recetox_aplcms_compute_clusters/0.13.2+galaxy0                               |     3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1                                                                         |     2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy3                                             |     2
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_align_features/recetox_aplcms_align_features/0.13.2+galaxy0                                   |     2
toolshed.g2.bx.psu.edu/repos/recetox/matchms_add_key/matchms_add_key/0.27.0+galaxy0                                                               |     2
__IMPORT_HISTORY__                                                                                                                                |     2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0                                                               |     2
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__CROSS_PRODUCT_NESTED__                                                                                                                          |     2
toolshed.g2.bx.psu.edu/repos/recetox/waveica/waveica/0.2.0+galaxy7                                                                                |     2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/abims_xcms_summary/3.12.0+galaxy0                                                           |     2
toolshed.g2.bx.psu.edu/repos/tomnl/mzml2isa/mzml2isa/1.1.1+galaxy1                                                                                |     2
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_template/recetox_aplcms_compute_template/0.12.0+galaxy2                               |     2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1                                                             |     2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0                                                       |     1
toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0                                                                                      |     1
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join1                                                                                                                                             |     1
__FILTER_EMPTY_DATASETS__                                                                                                                         |     1
CONVERTER_gz_to_uncompressed                                                                                                                      |     1
CONVERTER_fastq_to_fqtoc0                                                                                                                         |     1
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_findrecalseries/mfassignr_findRecalSeries/1.1.2+galaxy1                                            |     1
toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_recallist/mfassignr_recallist/1.1.2+galaxy0                                                        |     1
toolshed.g2.bx.psu.edu/repos/recetox/matchms_split/matchms_split/0.27.0+galaxy0                                                                   |     1
toolshed.g2.bx.psu.edu/repos/recetox/matchms_spectral_similarity/matchms_spectral_similarity/0.27.0+galaxy0                                       |     1
toolshed.g2.bx.psu.edu/repos/recetox/matchms_remove_spectra/matchms_remove_spectra/0.27.0+galaxy0                                                 |     1
toolshed.g2.bx.psu.edu/repos/recetox/matchms_metadata_match/matchms_metadata_match/0.27.0+galaxy0                                                 |     1
comp1                                                                                                                                             |     1
toolshed.g2.bx.psu.edu/repos/recetox/matchms_formatter/matchms_formatter/0.27.0+galaxy0                                                           |     1
toolshed.g2.bx.psu.edu/repos/recetox/recetox_aplcms_compute_template/recetox_aplcms_compute_template/0.13.2+galaxy0                               |     1
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0                                                                      |     1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0                                                             |     1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0                                             |     1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0                                                                     |     1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy1                                                       |     1