Mercurial > repos > bgruening > create_tool_recommendation_model
comparison test-data/test_tool_usage @ 5:4f7e6612906b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 5eebc0cb44e71f581d548b7e842002705dd155eb"
| author | bgruening |
|---|---|
| date | Fri, 06 May 2022 09:05:18 +0000 |
| parents | 5b3c08710e47 |
| children | e94dc7945639 |
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| 4:afec8c595124 | 5:4f7e6612906b |
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| 1 toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.1 2020-04-01 34568 | 1 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6 2022-02-01 50054 |
| 2 upload1 2020-04-01 18321 | 2 upload1 2022-02-01 43169 |
| 3 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 2020-04-01 2839 | 3 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 2022-02-01 39139 |
| 4 toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring/0.2.0 2020-04-01 1220 | 4 Cut1 2022-02-01 29046 |
| 5 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 2020-04-01 958 | 5 toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 2022-02-01 27481 |
| 6 CONVERTER_gz_to_uncompressed 2020-04-01 919 | 6 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.1+galaxy2 2022-02-01 17579 |
| 7 Filter1 2020-04-01 800 | 7 toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0 2022-02-01 15902 |
| 8 Cut1 2020-04-01 787 | 8 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 2022-02-01 14479 |
| 9 __SET_METADATA__ 2020-04-01 685 | 9 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 2022-02-01 13513 |
| 10 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 2020-04-01 643 | 10 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy0 2022-02-01 13197 |
| 11 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1 2020-04-01 627 | 11 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_annotate/bcftools_annotate/1.10 2022-02-01 13176 |
| 12 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.2b 2020-04-01 605 | 12 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0 2022-02-01 12931 |
| 13 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 2020-04-01 538 | 13 Filter1 2022-02-01 12490 |
| 14 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.2.0.1 2020-04-01 530 | 14 __UNZIP_COLLECTION__ 2022-02-01 12042 |
| 15 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 2020-04-01 475 | 15 toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 2022-02-01 11810 |
| 16 Remove beginning1 2020-04-01 447 | 16 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 2022-02-01 11502 |
| 17 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 2020-04-01 408 | 17 toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc3+galaxy0 2022-02-01 11487 |
| 18 join1 2020-04-01 369 | 18 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 2022-02-01 10705 |
| 19 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5 2020-04-01 357 | 19 toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 2022-02-01 10569 |
| 20 Convert characters1 2020-04-01 351 | 20 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 2022-02-01 10545 |
| 21 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3 2020-04-01 336 | 21 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 2022-02-01 10543 |
| 22 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 2020-04-01 316 | 22 toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2 2022-02-01 10456 |
| 23 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.29.0 2020-04-01 313 | 23 toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2 2022-02-01 9307 |
| 24 toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 2020-04-01 311 | 24 toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 2022-02-01 9275 |
| 25 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 2020-04-01 305 | 25 toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1 2022-02-01 9066 |
| 26 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 2020-04-01 302 | 26 toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0 2022-02-01 9055 |
| 27 cat1 2020-04-01 299 | 27 toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0 2022-02-01 9038 |
| 28 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6 2020-04-01 298 | 28 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.29.2 2022-02-01 9036 |
| 29 addValue 2020-04-01 294 | 29 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1 2022-02-01 9001 |
| 30 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0 2020-04-01 276 | 30 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 2022-02-01 7639 |
| 31 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2020-04-01 275 | 31 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10+galaxy1 2022-02-01 7325 |
| 32 toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2 2020-04-01 274 | 32 toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 2022-02-01 7256 |
| 33 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7.1 2020-04-01 274 | 33 toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_reheader/0.1.8_1 2022-02-01 7238 |
| 34 ebi_sra_main 2020-04-01 272 | 34 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 2022-02-01 7178 |
| 35 Grouping1 2020-04-01 237 | 35 toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy2 2022-02-01 6751 |
| 36 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 2020-04-01 236 | 36 __FILTER_FAILED_DATASETS__ 2022-02-01 6565 |
| 37 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1 2020-04-01 233 | 37 toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 2022-02-01 6529 |
| 38 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 2020-04-01 220 | 38 toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy2 2022-02-01 6479 |
| 39 toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1 2020-04-01 219 | 39 toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0 2022-02-01 6397 |
| 40 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4+galaxy1 2020-04-01 218 | 40 toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0 2022-02-01 4890 |
| 41 toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.1 2020-04-01 216 | 41 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.1 2022-02-01 4702 |
| 42 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 2020-04-01 216 | 42 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 2022-02-01 4646 |
| 43 toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/3.0.0 2020-04-01 209 | 43 toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.5+galaxy4 2022-02-01 4429 |
| 44 toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5 2020-04-01 204 | 44 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2022-02-01 4240 |
| 45 toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0 2020-04-01 187 | 45 toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.8a 2022-02-01 4099 |
| 46 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1+galaxy0 2020-04-01 185 | 46 toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 2022-02-01 3694 |
| 47 CONVERTER_interval_to_bed_0 2020-04-01 182 | 47 __DATA_FETCH__ 2022-02-01 3686 |
| 48 toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1 2020-04-01 178 | 48 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.24+galaxy0 2022-02-01 3234 |
| 49 ucsc_table_direct1 2020-04-01 177 | 49 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 2022-02-01 2936 |
| 50 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1 2020-04-01 176 | 50 toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0 2022-02-01 2814 |
| 51 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5 2020-04-01 175 | 51 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy0 2022-02-01 2759 |
| 52 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 2020-04-01 172 | 52 toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.3.1+galaxy0 2022-02-01 2442 |
| 53 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4 2020-04-01 169 | 53 toolshed.g2.bx.psu.edu/repos/iuc/ivar_removereads/ivar_removereads/1.3.1+galaxy0 2022-02-01 2389 |
| 54 toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5 2020-04-01 167 | 54 CONVERTER_gz_to_uncompressed 2022-02-01 2340 |
| 55 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1 2020-04-01 159 | 55 Grouping1 2022-02-01 2333 |
| 56 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1 2020-04-01 156 | 56 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.30.0 2022-02-01 2288 |
| 57 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0 2020-04-01 150 | 57 sort1 2022-02-01 1937 |
| 58 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4 2020-04-01 147 | 58 toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1 2022-02-01 1837 |
| 59 toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0 2020-04-01 143 | 59 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10 2022-02-01 1793 |
| 60 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.3.2.0.0 2020-04-01 143 | 60 toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0 2022-02-01 1782 |
| 61 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0 2020-04-01 143 | 61 toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 2022-02-01 1769 |
| 62 toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 2020-04-01 142 | 62 toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.6+galaxy1 2022-02-01 1718 |
| 63 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 2020-04-01 139 | 63 toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 2022-02-01 1446 |
| 64 toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.3 2020-04-01 136 | 64 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 2022-02-01 1435 |
| 65 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1 2020-04-01 134 | 65 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7+galaxy1 2022-02-01 1432 |
| 66 wig_to_bigWig 2020-04-01 121 | 66 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0 2022-02-01 1360 |
| 67 trimmer 2020-04-01 121 | 67 toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/2.0 2022-02-01 1291 |
| 68 toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0 2020-04-01 120 | 68 __SET_METADATA__ 2022-02-01 1260 |
| 69 CONVERTER_fastq_to_fqtoc0 2020-04-01 117 | 69 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 2022-02-01 1036 |
| 70 CONVERTER_bz2_to_uncompressed 2020-04-01 115 | 70 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 2022-02-01 1019 |
| 71 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1 2020-04-01 112 | 71 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 2022-02-01 973 |
| 72 toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/5.0.5.0 2020-04-01 110 | 72 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 2022-02-01 962 |
| 73 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.3 2020-04-01 110 | 73 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1 2022-02-01 926 |
| 74 toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0 2020-04-01 107 | 74 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.3.2.0.0 2022-02-01 915 |
| 75 toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 2020-04-01 105 | 75 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 2022-02-01 907 |
| 76 toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 2020-04-01 105 | 76 toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13 2022-02-01 897 |
| 77 toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 2020-04-01 103 | 77 toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 2022-02-01 879 |
| 78 comp1 2020-04-01 102 | 78 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy0 2022-02-01 871 |
| 79 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0 2020-04-01 101 | 79 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.2+galaxy0 2022-02-01 862 |
| 80 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 2020-04-01 98 | 80 cat1 2022-02-01 795 |
| 81 toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.3 2020-04-01 98 | 81 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 2022-02-01 772 |
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| 88 toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0 2020-04-01 86 | 88 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy1 2022-02-01 606 |
| 89 toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 2020-04-01 84 | 89 toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 2022-02-01 588 |
| 90 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/1.2.1 2020-04-01 82 | 90 join1 2022-02-01 584 |
| 91 toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 2020-04-01 82 | 91 toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.5 2022-02-01 580 |
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| 93 toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 2020-04-01 79 | 93 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1+galaxy1 2022-02-01 544 |
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