jennaj

Done

 Mappers label BAM output with fastq dbkey, not aligned genome dbkey. These are tool problems. Do we want one ticket or a group ticket? Not sure how many tools are impacted. galaxyproject/usegalaxy-playbook#104 && roadmap https://github.com/galaxyproject/galaxy/projects/8#card-8416292. 5/25 retest on main, still fails to assign the genome actually aligned against. Inherits database based on fastq input (if assigned) or produces "?" database if fasta does not have database assigned.
 Related to bam datatypes, new ticket for IUC to consider tool upgrades galaxyproject/tools-iuc#1774
 Test new bam datatypes First tests pass (bam, unsorted.bam) galaxyproject/usegalaxy-playbook#102
 Test updated Genome Space importer/exporter once active again on main galaxyproject/usegalaxy-playbook#100 (prior update: galaxyproject/usegalaxy-playbook#92). 5/17 retest - Just the importer is failing now, exporter good. 5/25 now works!
 SamToFastq noodle connection problems when used in workflow. From 11/2016! 5/30 retest in p

jennaj

================================================= ================ Tool ID Version ================================================= ================ bam_to_sam 2.0.1 bam_to_scidx 1.0.1 bamSplit 2.4.0 bedtools_coveragebed 2.27 bedtools_intersectbed 2.27 bg_diamond 0.8.24.1 bg_diamond_makedb 0.8.24

jennaj

{"status": "done", "can_manage_dataset": false, "display_name": "Bowtie2 on data 363 and data 362: aligned reads (sorted BAM)", "permission_inputs": [{"inputs": [{"readonly": true, "type": "text", "name": "olivier.buhard@inserm.frmanage permissions", "value": "olivier.buhard@inserm.fr", "label": "Users having associated role can manage the roles associated with permissions on this dataset."}], "type": "section", "name": "manage permissions", "label": "manage permissions"}], "convert_datatype_inputs": [{"help": "This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.", "value": ["bam"], "label": "New Type:", "type": "select", "options": [["ab1", "ab1"], ["acedb", "acedb"], ["afg", "afg"], ["arff", "arff"], ["asn1", "asn1"], ["asn1-binary", "asn1-binary"], ["augustus", "augustus"], ["axt", "axt"], ["bam", "bam"], ["bcf", "bcf"], ["bcf_bgzip", "bcf_bgzip"], ["bcf_uncompressed", "bcf_uncompressed"], ["bed", "bed"], ["b

jennaj

{"status": "done", "can_manage_dataset": false, "display_name": "Bowtie2 on data 363 and data 362: aligned reads (sorted BAM)", "permission_inputs": [{"inputs": [{"readonly": true, "type": "text", "name": "olivier.buhard@inserm.frmanage permissions", "value": "olivier.buhard@inserm.fr", "label": "Users having associated role can manage the roles associated with permissions on this dataset."}], "type": "section", "name": "manage permissions", "label": "manage permissions"}], "convert_datatype_inputs": [{"help": "This will change the datatype of the existing dataset but not modify its contents. Use this if Galaxy has incorrectly guessed the type of your dataset.", "value": ["bam"], "label": "New Type:", "type": "select", "options": [["ab1", "ab1"], ["acedb", "acedb"], ["afg", "afg"], ["arff", "arff"], ["asn1", "asn1"], ["asn1-binary", "asn1-binary"], ["augustus", "augustus"], ["axt", "axt"], ["bam", "bam"], ["bcf", "bcf"], ["bcf_bgzip", "bcf_bgzip"], ["bcf_uncompressed", "bcf_uncompressed"], ["bed", "bed"], ["b