| Previous changeset 4:ea93df4b3df2 (2024-10-17) Next changeset 6:dfd6fa2637ba (2025-06-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 164bcc563f8495d4bb1ce14b574aef9287904f40 |
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modified:
macro.xml tooldistillator.xml |
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added:
test-data/checkm2/DIAMOND_RESULTS.tsv test-data/checkm2/checkm2.log test-data/checkm2/quality_report.tsv |
| b |
| diff -r ea93df4b3df2 -r 66617be450bd macro.xml --- a/macro.xml Thu Oct 17 08:00:15 2024 +0000 +++ b/macro.xml Thu Apr 10 15:02:10 2025 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.9.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">0.9.2</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command><![CDATA[tooldistillator --version]]></version_command> |
| b |
| diff -r ea93df4b3df2 -r 66617be450bd test-data/checkm2/DIAMOND_RESULTS.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/checkm2/DIAMOND_RESULTS.tsv Thu Apr 10 15:02:10 2025 +0000 |
| b |
| b'@@ -0,0 +1,100 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No newline at end of file\n' |
| b |
| diff -r ea93df4b3df2 -r 66617be450bd test-data/checkm2/checkm2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/checkm2/checkm2.log Thu Apr 10 15:02:10 2025 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +[03/03/2025 11:20:03 AM] INFO: Running CheckM2 version 1.0.2 +[03/03/2025 11:20:03 AM] INFO: Custom database path provided for predict run. Checking database at Database/CheckM2_database/uniref100.KO.1.dmnd... +[03/03/2025 11:20:10 AM] INFO: Running quality prediction workflow with 5 threads. +[03/03/2025 11:20:12 AM] INFO: Calling genes in 50 bins with 5 threads: +[03/03/2025 11:20:59 AM] WARNING: Skipping protein file batches/batch_0/checkm2/protein_files/bin_concoct_SASB_HSMA33OT.11.faa as it was empty. +[03/03/2025 11:20:59 AM] INFO: Calculating metadata for 49 bins with 5 threads: +[03/03/2025 11:20:59 AM] INFO: Annotating input genomes with DIAMOND using 5 threads +[03/03/2025 11:23:40 AM] INFO: Processing DIAMOND output +[03/03/2025 11:23:40 AM] INFO: Predicting completeness and contamination using ML models. +[03/03/2025 11:23:44 AM] INFO: Parsing all results and constructing final output table. +[03/03/2025 11:23:44 AM] INFO: CheckM2 finished successfully. |
| b |
| diff -r ea93df4b3df2 -r 66617be450bd test-data/checkm2/quality_report.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/checkm2/quality_report.tsv Thu Apr 10 15:02:10 2025 +0000 |
| b |
| @@ -0,0 +1,50 @@ +Name Completeness Contamination Completeness_Model_Used Translation_Table_Used Coding_Density Contig_N50 Average_Gene_Length Genome_Size GC_Content Total_Coding_Sequences Total_Contigs Max_Contig_Length Additional_Notes +bin_concoct_SASB_CSM7KOLE.0 22.51 0.0 Neural Network (Specific Model) 11 0.887 2144 267.22576530612247 708085 0.53 784 324 5294 None +bin_concoct_SASB_CSM7KOLE.1 15.91 5.09 Neural Network (Specific Model) 11 0.845 4814 222.07713884992987 1119464 0.47 1426 273 50470 None +bin_concoct_SASB_CSM7KOLE.20 6.38 0.0 Gradient Boost (General Model) 11 0.974 3001 300.0 16618 0.61 18 6 4049 None +bin_concoct_SASB_CSM7KOLE.22 100.0 2.05 Neural Network (Specific Model) 11 0.87 22717 300.98043641835966 2755022 0.54 2658 187 146684 None +bin_concoct_SASB_CSM7KOLE.24 6.38 0.0 Gradient Boost (General Model) 11 0.926 5194 268.5 5194 0.45 6 1 5194 None +bin_concoct_SASB_CSM7KOLE.3 6.38 0.0 Gradient Boost (General Model) 11 0.818 4650 264.75 7724 0.36 8 3 4650 None +bin_concoct_SASB_CSM7KOLE.30 6.38 0.0 Gradient Boost (General Model) 11 0.796 1887 501.0 1887 0.5 1 1 1887 None +bin_concoct_SASB_HSMA33MG.1 33.58 0.68 Neural Network (Specific Model) 11 0.856 2959 250.53061224489795 987394 0.59 1127 345 13858 None +bin_concoct_SASB_HSMA33MG.10 6.38 0.0 Gradient Boost (General Model) 11 0.998 2318 386.0 2318 0.36 2 1 2318 None +bin_concoct_SASB_HSMA33MG.12 9.66 0.29 Neural Network (Specific Model) 11 0.887 1956 238.57806691449815 432765 0.41 538 204 12095 None +bin_concoct_SASB_HSMA33MG.13 6.65 0.0 Gradient Boost (General Model) 11 0.936 1726 269.5 1726 0.45 2 1 1726 None +bin_concoct_SASB_HSMA33MG.8 6.38 0.0 Gradient Boost (General Model) 11 0.794 1759 233.0 1759 0.53 2 1 1759 None +bin_concoct_SASB_HSMA33MG.9 53.69 21.09 Neural Network (Specific Model) 11 0.901 2957 269.85174585002864 3130308 0.44 3494 1086 18806 None +bin_concoct_SASB_HSMA33OT.0 4.43 0.0 Neural Network (Specific Model) 11 0.851 1985 214.93157894736842 143344 0.38 190 71 3816 None +bin_concoct_SASB_HSMA33OT.10 6.38 0.0 Gradient Boost (General Model) 11 0.966 11244 210.76666666666668 19477 0.36 30 4 11244 None +bin_concoct_SASB_HSMA33OT.14 6.38 0.0 Gradient Boost (General Model) 11 0.509 1707 290.0 1707 0.44 1 1 1707 None +bin_concoct_SASB_HSMA33OT.16 9.03 0.06 Neural Network (Specific Model) 11 0.881 1824 231.57877813504822 244747 0.42 311 130 3723 None +bin_concoct_SASB_HSMA33OT.18 6.38 0.0 Gradient Boost (General Model) 11 0.958 1602 256.0 1602 0.36 2 1 1602 None +bin_concoct_SASB_HSMA33OT.2 6.38 0.0 Gradient Boost (General Model) 11 0.941 1704 345.0 3299 0.35 3 2 1704 None +bin_concoct_SASB_HSMA33OT.3 5.64 0.0 Gradient Boost (General Model) 11 0.839 2532 203.5 4366 0.44 6 2 2532 None +bin_concoct_SASB_HSMA33OT.4 6.38 0.0 Gradient Boost (General Model) 11 0.634 2866 202.0 2866 0.42 3 1 2866 None +bin_concoct_SASB_HSMA33OT.6 6.42 0.0 Gradient Boost (General Model) 11 0.915 1816 233.42857142857142 10707 0.61 14 6 2097 None +bin_concoct_SASB_MSM5LLDE.16 6.38 0.0 Gradient Boost (General Model) 11 0.998 1592 530.0 1592 0.6 1 1 1592 None +bin_concoct_SASB_MSM5LLDE.19 6.38 0.0 Gradient Boost (General Model) 11 0.819 1941 68.75 1941 0.39 8 1 1941 None +bin_concoct_SASB_MSM5LLDE.2 6.38 0.0 Gradient Boost (General Model) 11 0.876 1618 236.5 1618 0.54 2 1 1618 None +bin_concoct_SASB_MSM5LLDE.20 49.54 0.72 Neural Network (Specific Model) 11 0.901 2559 261.2743158588856 2632930 0.42 3033 1029 33333 None +bin_concoct_SASB_MSM5LLDE.21 99.55 8.64 Neural Network (Specific Model) 11 0.9 81127 346.90618336886996 4332951 0.46 3752 143 235469 None +bin_concoct_SASB_MSM5LLDE.27 9.51 0.07 Neural Network (Specific Model) 11 0.877 1958 217.07469879518072 307709 0.57 415 150 5816 None +bin_concoct_SASB_MSM5LLDE.28 6.38 0.0 Gradient Boost (General Model) 11 0.952 1638 260.0 1638 0.59 2 1 1638 None +bin_concoct_SASB_MSM5LLDE.6 5.91 0.0 Gradient Boost (General Model) 11 0.91 1987 228.10714285714286 20991 0.61 28 11 2365 None +bin_concoct_SASB_MSM5LLDE.7 5.03 0.0 Gradient Boost (General Model) 11 0.999 1689 282.0 1689 0.65 2 1 1689 None +bin_metabat_SASB_CSM7KOLE.10 45.04 8.76 Neural Network (Specific Model) 11 0.903 2382 261.277639046538 3814277 0.41 4405 1544 17510 None +bin_metabat_SASB_CSM7KOLE.2 18.36 0.04 Neural Network (Specific Model) 11 0.924 2177 272.32474226804123 514039 0.49 582 230 4454 None +bin_metabat_SASB_CSM7KOLE.3 15.42 0.06 Neural Network (Specific Model) 11 0.944 2547 288.0351906158358 623088 0.49 682 253 7390 None +bin_metabat_SASB_CSM7KOLE.7 5.83 0.18 Neural Network (Specific Model) 11 0.906 146684 275.6360153256705 237533 0.52 261 10 146684 None +bin_metabat_SASB_MSM5LLDE.1 85.75 0.14 Neural Network (Specific Model) 11 0.897 81302 343.6424261670372 3612719 0.46 3149 65 235469 None +bin_metabat_SASB_MSM5LLDE.2 96.34 0.33 Neural Network (Specific Model) 11 0.866 76315 307.9110091743119 2321808 0.57 2180 40 221393 None +bin_semibin_SASB_CSM7KOLE.0 17.68 0.13 Neural Network (Specific Model) 11 0.895 3290 276.360396039604 467082 0.59 505 137 14331 None +bin_semibin_SASB_CSM7KOLE.1 45.77 0.88 Gradient Boost (General Model) 11 0.901 4330 318.24455825864277 1653306 0.5 1562 386 16396 None +bin_semibin_SASB_CSM7KOLE.10 10.46 0.46 Neural Network (Specific Model) 11 0.884 8223 264.5268817204301 749398 0.39 837 118 30972 None +bin_semibin_SASB_CSM7KOLE.11 14.55 3.97 Neural Network (Specific Model) 11 0.89 19781 259.4004424778761 788274 0.5 904 74 146684 None +bin_semibin_SASB_CSM7KOLE.14 92.78 0.09 Neural Network (Specific Model) 11 0.897 65685 352.9744467860906 4474676 0.42 3796 113 353143 None +bin_semibin_SASB_CSM7KOLE.16 10.61 0.0 Neural Network (Specific Model) 11 0.881 3151 281.17182130584195 278023 0.52 291 84 5610 None +bin_semibin_SASB_CSM7KOLE.3 10.48 1.74 Neural Network (Specific Model) 11 0.919 3218 322.7874125874126 752315 0.41 715 228 6603 None +bin_semibin_SASB_HSMA33MG.1 37.55 7.85 Neural Network (Specific Model) 11 0.909 3945 314.83505866114564 1502934 0.43 1449 378 18770 None +bin_semibin_SASB_HSMA33MG.2 9.86 0.19 Neural Network (Specific Model) 11 0.84 5391 209.15863141524105 478276 0.48 643 94 18806 None +bin_semibin_SASB_MSM5LLDE.0 6.09 0.04 Neural Network (Specific Model) 11 0.889 3492 214.14640198511165 290530 0.54 403 76 32205 None +bin_semibin_SASB_MSM5LLDE.1 29.89 0.02 Neural Network (Specific Model) 11 0.914 3803 319.14351851851853 1129847 0.42 1080 302 10395 None +bin_semibin_SASB_MSM5LLDE.10 6.39 0.04 Neural Network (Specific Model) 11 0.838 6460 243.23076923076923 214350 0.48 247 38 17791 None |
| b |
| diff -r ea93df4b3df2 -r 66617be450bd tooldistillator.xml --- a/tooldistillator.xml Thu Oct 17 08:00:15 2024 +0000 +++ b/tooldistillator.xml Thu Apr 10 15:02:10 2025 +0000 |
| b |
| b'@@ -118,6 +118,19 @@\n --threshold \'$tool.select_tool.threshold\'\n --read_len \'$tool.select_tool.read_len\'\n --level \'$tool.select_tool.level\'\n+ #elif $tool.select_tool.tool_list == \'checkm2\':\n+ #if $tool.select_tool.diamond_results_path\n+ --diamond_results_path \'$tool.select_tool.diamond_results_path\'\n+ --diamond_results_hid \'$tool.select_tool.diamond_results_path.hid\'\n+ #end if\n+ #if $tool.select_tool.protein_zip_path\n+ --protein_zip_path \'$tool.select_tool.protein_zip_path\'\n+ --protein_zip_hid \'$tool.select_tool.protein_zip_path.hid\'\n+ #end if\n+ #if $tool.select_tool.checkm2_log_path\n+ --checkm2_log_path \'$tool.select_tool.checkm2_log_path\'\n+ --checkm2_log_hid \'$tool.select_tool.checkm2_log_path.hid\'\n+ #end if\n #elif $tool.select_tool.tool_list == \'fastp\':\n #if $tool.select_tool.trimmed_forward_R1_path\n --trimmed_forward_R1_path \'$tool.select_tool.trimmed_forward_R1_path\'\n@@ -251,6 +264,7 @@\n <option value="bandage">Bandage</option>\n <option value="bracken">Bracken</option>\n <option value="bwa">BWA</option>\n+ <option value="checkm2">CheckM2</option>\n <option value="fastp">Fastp</option>\n <option value="fastqc">Fastqc</option>\n <option value="filtlong">Filtlong</option>\n@@ -326,6 +340,14 @@\n <expand macro="analysis_software_version"/>\n <expand macro="reference_database_version"/>\n </when>\n+ <when value="checkm2">\n+ <param name="input" type="data" format="txt,tabular" multiple="false" label="CheckM2 quality report file" help="Tabular file from CheckM2 output"/>\n+ <param argument="--diamond_results_path" type="data" format="txt,tabular" optional="true" multiple="false" label="CheckM2 Diamond results file" help="DIAMOND_RESULTS file for CheckM2"/>\n+ <param argument="--protein_zip_path" type="data" format="zip,tar,tar.gz" optional="true" multiple="false" label="Archive file with protein files from CheckM2" help="Protein sequence fasta files in an archive file for CheckM2"/>\n+ <param argument="--checkm2_log_path" type="data" format="txt" multiple="false" optional="true" label="CheckM2 log file" help="Log file from CheckM2"/>\n+ <expand macro="analysis_software_version"/>\n+ <expand macro="reference_database_version"/>\n+ </when>\n <when value="fastp">\n <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>\n <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/>\n@@ -597,6 +619,19 @@\n </repeat>\n <repeat name="tools">\n <conditional name="select_tool">\n+ <param name="tool_list" value="checkm2"/>\n+ <param name="input" value="checkm2/quality_report.tsv" ftype="tabular"/>\n+ <param name="diamond_results_path" value="checkm2/DIAMOND_RESULTS.tsv"/>\n+ <param name="checkm2_log_path" value="checkm2/checkm2.log"/>\n+ <conditional name="origin">\n+ <param name="origin" value="true"/>\n+ <param name="analysis_software_version" value="1.0.2"/>\n+ </conditional>\n+ <param name="reference_database_version" value="Uniref"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="tools">\n+ '..b'691"/>\n+ <expand macro="element_assert" name="checkm2_6_output" text="UniRef100_B5R745"/>\n+ <expand macro="element_assert" name="fastp_7_output" text="705053822"/>\n+ <expand macro="element_assert" name="fastqc_8_output" text="Sequences flagged as poor quality"/>\n+ <expand macro="element_assert" name="filtlong_9_output" text="filtlong_report"/>\n+ <expand macro="element_assert" name="flye_10_output" text="contig_2"/>\n+ <expand macro="element_assert" name="integronfinder2_11_output" text="2353.0"/>\n+ <expand macro="element_assert" name="isescan_12_output" text="IS200/IS605"/>\n+ <expand macro="element_assert" name="kraken2_13_output" text="Enterococcus_faecalis"/>\n+ <expand macro="element_assert" name="plasmidfinder_14_output" text="repUS40_1_repB"/>\n+ <expand macro="element_assert" name="polypolish_15_output" text="320811"/>\n+ <expand macro="element_assert" name="quast_16_output" text="2944723"/>\n+ <expand macro="element_assert" name="recentrifuge_17_output" text="6.4917947578"/>\n+ <expand macro="element_assert" name="refseqmasher_18_output" text="GCF_000519925.1"/>\n+ <expand macro="element_assert" name="shovill_19_output" text="436224"/>\n+ <expand macro="element_assert" name="tabular_file_20_output" text="NP_814691"/>\n </output_collection>\n </test>\n </tests>\n@@ -801,9 +837,10 @@\n ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.\n \n This tool here is extracting information from output files of specific tools and exposing it as JSON files\n+\n ** Tool input**\n \n-ToolDistillator can use several input type from at least 21 different tools and 1 generic tool for tabular file:\n+ToolDistillator can use several input type from at least 22 different tools and 1 generic tool for tabular file:\n \n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Tools | Version | Default input file| Optional files |\n@@ -820,6 +857,8 @@\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | BWA | 2.2.1 | input1.bam | input2.bam |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n+| CheckM2 |1.0.2 | quality_report.tsv| DIAMOND_RESULTS.tsv, protein_files.zip, checkm2.log |\n++----------------+----------------+-------------------+------------------------------------------------------------+\n | Fastp | 0.23.2 | output.json | |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Fastqc | 0.12.1 | report.txt | report.html |\n@@ -850,7 +889,7 @@\n +----------------+----------------+-------------------+------------------------------------------------------------+\n | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n-| tabular_file | 0 | output.tsv | no optional files |\n+| tabular_file | 0 | output.tsv | |\n +----------------+----------------+-------------------+------------------------------------------------------------+\n \n ** Options **\n' |