From 3486b90d81989bfae6d097b1b18957aff0802abd Mon Sep 17 00:00:00 2001 From: iwc-workflows-bot Date: Thu, 14 Mar 2024 15:35:15 +0000 Subject: [PATCH] Update for version 0.10 --- .github/workflows/wftest.yml | 4 +- CHANGELOG.md | 11 ++++ atacseq-tests.yml | 24 ++++---- atacseq.ga | 103 +++++++++++++++++------------------ ro-crate-metadata.json | 6 +- 5 files changed, 77 insertions(+), 71 deletions(-) diff --git a/.github/workflows/wftest.yml b/.github/workflows/wftest.yml index 1344d7a..b0e927d 100644 --- a/.github/workflows/wftest.yml +++ b/.github/workflows/wftest.yml @@ -10,7 +10,7 @@ jobs: with: python-version-list: "[\"3.7\"]" galaxy-fork: galaxyproject - galaxy-branch: release_23.1 + galaxy-branch: release_23.2 test: name: Test workflow needs: setup @@ -19,6 +19,6 @@ jobs: galaxy-head-sha: ${{ needs.setup.outputs.galaxy-head-sha }} python-version-list: "[\"3.7\"]" galaxy-fork: galaxyproject - galaxy-branch: release_23.1 + galaxy-branch: release_23.2 repository-list: '.' check-outputs: true diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c3ce30..5417d4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,16 @@ # Changelog +## [0.10] 2024-03-14 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1` +- `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5` +- `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0` + ## [0.9] 2023-10-23 Fix the normalization factor. It was coverage per reads and per reads in peaks instead of per million reads and per million reads in peaks. diff --git a/atacseq-tests.yml b/atacseq-tests.yml index 49d1939..3481b4a 100644 --- a/atacseq-tests.yml +++ b/atacseq-tests.yml @@ -25,11 +25,11 @@ SRR891268_chr22_enriched: asserts: - that: "has_text" - text: "32872 (11.70%) aligned concordantly 0 times" + text: "30410 (10.82%) aligned concordantly 0 times" - that: "has_text" - text: "108014 (38.44%) aligned concordantly exactly 1 time" + text: "109333 (38.91%) aligned concordantly exactly 1 time" - that: "has_text" - text: "140078 (49.86%) aligned concordantly >1 times" + text: "141221 (50.26%) aligned concordantly >1 times" MarkDuplicates metrics: element_tests: SRR891268_chr22_enriched: @@ -55,7 +55,7 @@ SRR891268_chr22_enriched: asserts: has_n_lines: - n: 225 + n: 223 MACS2 report: element_tests: SRR891268_chr22_enriched: @@ -63,7 +63,7 @@ - that: "has_text" text: "# tag size is determined as 47 bps" - that: "has_text" - text: "# total tags in treatment: 234432" + text: "# total tags in treatment: 232804" Coverage from MACS2 (bigwig): element_tests: SRR891268_chr22_enriched: @@ -76,13 +76,13 @@ SRR891268_chr22_enriched: asserts: has_n_lines: - n: 213 + n: 211 Nb of reads in summits +-500bp: element_tests: SRR891268_chr22_enriched: asserts: has_line: - line: "8802" + line: "8698" bigwig_norm: element_tests: SRR891268_chr22_enriched: @@ -102,23 +102,23 @@ bowtie2: asserts: has_line: - line: "SRR891268_chr22_enriched\t280964\t280964\t32872\t108014\t140078\t13586\t6283\t7890\t24399\t98.88\t12199.5\t3141.5\t3945.0" + line: "SRR891268_chr22_enriched\t280964\t280964\t30410\t109333\t141221\t13319\t6127\t6515\t21540\t98.91\t10770.0\t3063.5\t3257.5" cutadapt: asserts: has_line: - line: "SRR891268_chr22_enriched_2\t4.4\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" + line: "SRR891268_chr22_enriched_2\t4.6\t285247\t41011\t40415\t4283\t280964\t28524700\t480633\t27163516\t4.771948521807416" general_stats: asserts: has_text: - text: "SRR891268_chr22_enriched\t200.0\t225\t0.028487\t98.88" + text: "SRR891268_chr22_enriched\t200.0\t223\t0.028469\t98.91" macs: asserts: has_line: - line: "SRR891268_chr22_enriched\t225\t47.0\t234432.0\t200.0" + line: "SRR891268_chr22_enriched\t223\t47.0\t232804.0\t200.0" picard_dups: asserts: has_line: - line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t120653.0\t0.0\t0.0\t0.0\t3437.0\t5.0\t0.028487\t2080211.0" + line: "SRR891268_chr22_enriched\tUnknown Library\t0.0\t119813.0\t0.0\t0.0\t0.0\t3411.0\t5.0\t0.028469\t2067029.0" sources: asserts: has_n_lines: diff --git a/atacseq.ga b/atacseq.ga index bc5ac77..5f69af4 100644 --- a/atacseq.ga +++ b/atacseq.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.9", + "release": "0.10", "name": "ATACseq", "steps": { "0": { @@ -123,7 +123,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1", "errors": null, "id": 4, "input_connections": { @@ -132,7 +132,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cutadapt", + "name": "library" + } + ], "label": "Cutadapt (remove adapter + bad quality bases)", "name": "Cutadapt", "outputs": [ @@ -168,15 +173,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1", "tool_shed_repository": { - "changeset_revision": "8c0175e03cee", + "changeset_revision": "64172f1c1202", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Nextera R2\", \"adapter2\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.4+galaxy0", + "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"RuntimeValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R1\", \"adapter\": \"CTGTCTCTTATACACATCTCCGAGCCCACGAGAC\"}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Nextera R2\", \"adapter\": \"CTGTCTCTTATACACATCTGACGCTGCCGACGA\"}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\", \"minimum_length2\": null, \"maximum_length2\": null}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"cut\": \"0\", \"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "4.6+galaxy1", "type": "tool", "uuid": "33fa2759-9f3f-431b-b35c-b5c777d5d5b7", "when": null, @@ -184,7 +189,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0", "errors": null, "id": 5, "input_connections": { @@ -235,15 +240,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "03e9b2fbc005", + "changeset_revision": "0d4acadabb04", "name": "bowtie2", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"--very-sensitive\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": false, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.5.0+galaxy0", + "tool_version": "2.5.3+galaxy0", "type": "tool", "uuid": "c32a3847-f673-487f-af98-8d50999f2d21", "when": null, @@ -318,7 +323,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "errors": null, "id": 7, "input_connections": { @@ -347,15 +352,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5", "tool_shed_repository": { - "changeset_revision": "7def34e6cf4d", + "changeset_revision": "fa5d3e61e429", "name": "samtools_idxstats", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.4", + "tool_version": "2.0.5", "type": "tool", "uuid": "024f7338-2712-4fb1-a913-dfd5bc2d4f1e", "when": null, @@ -363,7 +368,7 @@ }, "8": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", "errors": null, "id": 8, "input_connections": { @@ -405,15 +410,15 @@ "output_name": "outFile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", "tool_shed_repository": { - "changeset_revision": "f9242e01365a", + "changeset_revision": "3f254c5ced1d", "name": "picard", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assume_sorted\": true, \"barcode_tag\": \"\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": true, \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.18.2.4", + "tool_version": "3.1.1.0", "type": "tool", "uuid": "d0a9998c-18a9-4579-8d33-f0897e1ceaeb", "when": null, @@ -432,7 +437,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -461,15 +466,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"code\": \" ($1==\\\"chrM\\\" || $1 == \\\"MT\\\"){print $1, $3}($1!=\\\"chrM\\\" && $1!=\\\"MT\\\"){SUM+=$3}END{print \\\"others\\\", SUM} \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "9ae38aa6-511d-4ab4-b055-7a1dae65649f", "when": null, @@ -591,7 +596,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", "errors": null, "id": 12, "input_connections": { @@ -620,15 +625,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", "tool_shed_repository": { - "changeset_revision": "5826298f6a73", + "changeset_revision": "6be888be75f9", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy0", + "tool_version": "1.15.1+galaxy2", "type": "tool", "uuid": "2999f836-c74f-47ed-b1ad-81f43349fe11", "when": null, @@ -775,12 +780,7 @@ "output_name": "outputcnt" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": "compute 1/million reads", "name": "Compute", "outputs": [ @@ -807,7 +807,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "ec62cddf-fb04-4185-b9f4-709de2ce0202", @@ -919,7 +919,7 @@ }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0", "errors": null, "id": 17, "input_connections": { @@ -957,15 +957,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"case_sensitive\": \"-i\", \"color\": \"NOCOLOR\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"invert\": \"\", \"lines_after\": \"0\", \"lines_before\": \"0\", \"regex_type\": \"-P\", \"url_paste\": \"^#\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.1", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "a12ee458-2fe0-4d1e-8df9-c8fc76d7b277", "when": null, @@ -1232,7 +1232,7 @@ }, "23": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "errors": null, "id": 23, "input_connections": { @@ -1270,15 +1270,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"code\": \"{S=S+$4}END{print S}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "f65b3936-595c-4ddb-88bc-2cc41e514e38", "when": null, @@ -1301,12 +1301,7 @@ "output_name": "outfile" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": "compute 1/million reads in peaks", "name": "Compute", "outputs": [ @@ -1333,7 +1328,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"avoid_scientific_notation\": true, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1000000/c1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"1\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0", "type": "tool", "uuid": "5f55e258-a4fe-4b51-ab9b-2a6f0f22d910", @@ -1424,7 +1419,7 @@ }, "27": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "errors": null, "id": 27, "input_connections": { @@ -1453,15 +1448,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "ddf54b12c295", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"code\": \" NR==1{print \\\"in peaks\\\",$1;inp=$1}NR==2{print \\\"outside peaks\\\",$1 - inp}\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "7fe2bb35-31b5-4da0-83cf-38bb4af2848e", "when": null, @@ -1625,6 +1620,6 @@ "tags": [ "ATACseq" ], - "uuid": "acfc2893-ea3c-429b-900f-6926ca7f04a5", + "uuid": "02785f0c-c445-4419-9f95-a202eaf6493a", "version": 1 } \ No newline at end of file diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index e68700a..e332c79 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,7 +21,7 @@ { "@id": "./", "@type": "Dataset", - "datePublished": "2023-10-23T15:16:21.551531", + "datePublished": "2024-03-14T15:35:04.671831", "hasPart": [ { "@id": "atacseq.ga" @@ -72,7 +72,7 @@ "@id": "#galaxy" }, "url": "https://github.com/iwc-workflows/atacseq", - "version": "0.9" + "version": "0.10" }, { "@id": "#galaxy", @@ -138,7 +138,7 @@ "conformsTo": { "@id": "https://w3id.org/ro/terms/test#PlanemoEngine" }, - "engineVersion": ">=0.75.14" + "engineVersion": ">=0.75.21" }, { "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",