search

seqcode / pegr

Platform for Eukaryotic Genome Regulation
MIT License
3 stars 1 forks source link

Annotate how data passed to the API is stored in PEGRdb #24

Closed grettadarmstrong closed 6 years ago

grettadarmstrong commented 6 years ago

Check the API and find which items are parsed and saved directly into the column fields for the sample row in the PEGRdb Analysis table, and which data item results are kept in the json dictionary bag and appended to the existing json bag that is stored for the sample row in the table.

We need to know this because data information that is always retrieved and displayed on the web pages for reporting or pulled for further downstream scripts, SHOULD be added into additional columns specifically on the Analysis table. Items that are unknown for future use may still remain or get appended to the json dictionary bag field (blob).

PrashantKuntala commented 6 years ago

We know that stats API endpoint for PEGR is being used by cegr output statistics and YEPQC pipeline to POST the JSON dictionaries to be stored in Analysis table in PEGRdb.

id version alignment_id category datasets note parameters statistics step_id tool date user_id step
int int int string JSON JSON JSON JSON galaxy_id galaxy_toolshed_version date_exec int step_name_in_pipeline
Category Tool name
output_fastqRead2 input_dataset_r2
output_fastqRead1 input_dataset_r1
output_fastqc toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.70
output_markDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1
output_samtoolFilter toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1
output_bamToScidx toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.1
output_peHistogram toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1
output_genetrack toolshed.g2.bx.psu.edu/repos/iuc/genetrack/genetrack/1.0.1
output_bedtoolsIntersect toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.0
output_cwpair2 toolshed.g2.bx.psu.edu/repos/iuc/cwpair2/cwpair2/1.1.0
output_extractGenomicDNA toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3
output_repeatMasker toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/0.1.2
output_meme toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.2.0
output_fimo toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0
output_fourColorPlot toolshed.g2.bx.psu.edu/repos/iuc/fasta_nucleotide_color_plot/fasta_nucleotide_color_plot/1.0.1
output_tagPileup toolshed.g2.bx.psu.edu/repos/iuc/tag_pileup_frequency/tag_pileup_frequency/1.0.1
output_bwaMem toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
Category Tool name
multiGPS 001
significanceTester 002
stamp 004
nucleosomeEnrichmentProfiler 005
pointEnrichmentTester 006
tableLookup 007
tapTagID 008
AMA-cs commented 6 years ago

Can you provide the keys/values of each JSON dictionary in some of the columns in the analysis table, please?

PrashantKuntala commented 6 years ago

scroll to the right to view the entire table :tada:

id version alignment_id category datasets note parameters statistics step_id tool date user_id step
131228 1 6468 output_fastqRead2 [{"type":"fastqsanger" "id":"37ab7a7a32401acf" "uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/37ab7a7a32401acf/display?preview=True"}] {"code":"OK"} [{}] input2 input_dataset_r2 2018-01-17 13:37:23 350 input_dataset_r2_output_stats
131229 1 6468 output_fastqRead1 [{"type":"fastqsanger" "id":"50a8478afaeabdf6" "uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/50a8478afaeabdf6/display?preview=True"}] {"code":"OK"} [{}] input1 input_dataset_r1 2018-01-17 13:37:23 350 input_dataset_r1_output_stats
131230 1 6468 output_fastqc [{"type":"html" "id":"aaea2e80d01a97d8" "uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/aaea2e80d01a97d8/display?preview=True"} {"type":"txt" "id":"6ebd0d567bfd2c23" "uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/6ebd0d567bfd2c23/display?preview=True"}] {"code":"OK"} {"limits":"null" "input_file":"{\"values\": [{\"src\": \"hda\" \"id\": 26689}]}" "workflow_invocation_uuid":"\"5476df74fbb511e7a807005056b99835\"" "dbkey":"\"sacCer3_cegr\"" "contaminants":"null" "chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{},{"read":2",adapterDimerCount":0.0}] 9c019bbfa7322549 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.70 2018-01-17 13:37:27 350 fastqc_output_stats
131244 1 6468 output_markDuplicates [{"type":"bam","id":"ebbf06fccbf90ae7","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/ebbf06fccbf90ae7/display?preview=True"}] {"code":"OK"} {"duplicate_scoring_strategy":"\"SUM_OF_BASE_QUALITIES\"","remove_duplicates":"\"false\"","comments":"[]","barcode_tag":"\"\"","optical_duplicate_pixel_distance":"\"100\"","workflow_invocation_uuid":"\"5476df74fbb511e7a807005056b99835\"","assume_sorted":"\"true\"","read_name_regex":"\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\"","dbkey":"\"sacCer3_cegr\"","validation_stringency":"\"LENIENT\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","inputFile":"{\"values\": [{\"src\": \"hda\", \"id\": 26698}]}"} [{"totalReads":1775045.0,"dedupUniquelyMappedReads":516636.0,"uniquelyMappedReads":1071695.0,"mappedReads":1242367.0}] 6bab45ab64c5184c toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1 2018-01-17 13:41:23 350 mark_duplicates_bam_output_stats
131245 1 6468 output_samtoolFilter [{"type":"bam","id":"9ed92f03267cbb80","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/9ed92f03267cbb80/display?preview=True"}] {"code":"OK"} {"bed_file":"null","workflow_invocation_uuid":"\"5476df74fbb511e7a807005056b99835\"","input1":"{\"values\": [{\"src\": \"hda\", \"id\": 26702}]}","read_group":"\"\"","dbkey":"\"sacCer3_cegr\"","regions":"\"\"","header":"\"-h\"","flag":"{\"filter\": \"yes\", \"skipBits\": [\"0x0004\", \"0x0400\"], \"__current_case__\": 1, \"reqBits\": [\"0x0001\"]}","mapq":"\"\"","library":"\"\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{}] 0d57d5e9c8f1b11b toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1 2018-01-17 13:41:34 350 samtool_filter2_output_stats
131248 1 6472 output_bamToScidx [{"type":"scidx","id":"de3ce28fb3988acd","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/de3ce28fb3988acd/display?preview=True"}] {"code":"OK"} {"dbkey":"\"sacCer3_cegr\"","require_proper_mate_pairing":"\"0\"","input_bam":"{\"values\": [{\"src\": \"hda\", \"id\": 26775}]}","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","min_insert_size":"\"\"","read":"\"0\"","max_insert_size":"\"\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{"genomeCoverage":0.0001}] 22252a9ba8aa001a toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.1 2018-01-17 13:41:56 350 bam_to_scidx_output_stats
131249 1 6472 output_peHistogram [{"type":"png","id":"b80e8ab4d0ab07b7","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/b80e8ab4d0ab07b7/display?preview=True"},{"type":"tabular","id":"c8040e4606a177e6","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/c8040e4606a177e6/display?preview=True"}] {"code":"OK"} {"chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","upper_limit":"\"\"","lower_limit":"\"\"","dbkey":"\"sacCer3_cegr\"","input_bam":"{\"values\": [{\"src\": \"hda\", \"id\": 26775}]}"} [{},{"avgInsertSize":113.6767,"stdDevInsertSize":59.289}] 0dd44cc0f0d96662 toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1 2018-01-17 13:41:56 350 pe_histogram_output_stats
131252 1 6472 output_genetrack [{"type":"gff","id":"a1d1c5ed7f6397b3","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/a1d1c5ed7f6397b3/display?preview=True"}] {"code":"OK"} {"workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","exclusion":"\"10\"","sigma":"\"5\"","down_width":"\"5\"","up_width":"\"5\"","filter":"\"0\"","dbkey":"\"sacCer3_cegr\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","input_format_cond":"{\"input\": {\"values\": [{\"src\": \"hda\", \"id\": 26777}]}, \"__current_case__\": 0, \"input_format\": \"scidx\"}"} [{"numberOfPeaks":1593,"peakMean":1.0100439422473322,"peakMeanStd":0.020401757689893284,"peakMedian":1.0,"singletons":1578,"peakMedianStd":0.0,"medianTagSingletons":1.0}] 6d8e2799fc4fbb6b toolshed.g2.bx.psu.edu/repos/iuc/genetrack/genetrack/1.0.1 2018-01-17 13:42:29 350 genetrack_output_stats
131253 1 6472 output_bedtoolsIntersect [{"type":"gff","id":"abe753e9ba6a8774","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/abe753e9ba6a8774/display?preview=True"}] {"code":"OK"} {"count":"\"false\"","reciprocal":"\"false\"","dbkey":"\"sacCer3_cegr\"","overlap_mode":"[\"-wa\"]","invert":"\"true\"","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","inputB":"{\"values\": [{\"src\": \"hda\", \"id\": 26759}]}","header":"\"false\"","inputA":"{\"values\": [{\"src\": \"hda\", \"id\": 26810}]}","split":"\"false\"","fraction":"\"\"","inputAXidentifier":"\"s5e10u5d5F0_on_data_17\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","strand":"\"\"","once":"\"false\""} [{"numberOfPeaks":1343,"peakMean":1.0007446016381236,"peakMeanStd":0.0,"peakMedian":1.0,"singletons":1343,"peakMedianStd":0.0,"medianTagSingletons":1.0}] 115edf925e26e651 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.0 2018-01-17 13:44:03 350 bedtools_intersectbed_output_stats
131271 1 6472 output_cwpair2 [{"type":"gff","id":"b4cf7a55ac605d81","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/b4cf7a55ac605d81/display?preview=True"}] {"code":"OK"} {"threshold_format_cond":"{\"relative_threshold\": \"0.0\", \"threshold_format\": \"relative_threshold\", \"__current_case\": 0}","workflow_invocation_uuid__":"\"d6c2a30afbb511e7b4d8005056b99835\"","binsize":"\"2\"","up_distance":"\"0\"","dbkey":"\"sacCer3_cegr\"","input":"{\"values\": [{\"src\": \"hdca\", \"id\": 10545}]}","down_distance":"\"80\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","method":"\"mode\"","output_files":"\"all\""} [{"peakPairWis":6}] d985782aa6a98b5f toolshed.g2.bx.psu.edu/repos/iuc/cwpair2/cwpair2/1.1.0 2018-01-17 13:46:08 350 cwpair2_output_stats
131278 1 6472 output_extractGenomicDNA [{"type":"fasta","id":"41cc7520c98880fd","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/41cc7520c98880fd/display?preview=True"}] {"code":"OK"} {"reference_genome_cond":"{\"reference_genome\": \"sacCer3_cegr\", \"reference_genome_source\": \"cached\", \"current_case__\": 0}","output_format_cond":"{\"fasta_header_type_cond\": {\"fasta_header_type\": \"bedtools_getfasta_default\", \"current_case\": 0}, \"output_format\": \"fasta\", \"__current_case\": 0}","interpret_features":"\"yes\"","inputXidentifier":"\"data_MP_mode_f0u0d80_on_data_26.gff\"","dbkey":"\"sacCer3_cegr\"","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","input":"{\"values\": [{\"src\": \"hda\", \"id\": 26899}]}","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{}] 7c1091413f383bdc toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3 2018-01-17 13:47:37 350 extract_genomic_dna_output_stats2
131288 1 6472 output_repeatMasker [{"type":"fasta","id":"4e8e59ec336fd376","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/4e8e59ec336fd376/display?preview=True"}] {"code":"OK"} {"nolow":"\"false\"","noint":"\"false\"","adv_opts":"{\"slow_search\": \"false\", \"current_case__\": 1, \"only_alus\": \"false\", \"adv_opts_selector\": \"advanced\", \"quick_search\": \"false\", \"gc\": \"0\", \"rush_search\": \"false\", \"is_only\": \"false\", \"gccalc\": \"true\", \"output_files\": [\"summary\", \"mask\"]}","queryXidentifier":"\"data_MP_mode_f0u0d80_on_data_26.gff\"","workflow_invocation_uuid__":"\"d6c2a30afbb511e7b4d8005056b99835\"","norna":"\"false\"","dbkey":"\"sacCer3_cegr\"","query":"{\"values\": [{\"src\": \"hda\", \"id\": 26900}]}","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","species":"\"-species fungi\""} [{}] 95fa410213cac0ea toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/0.1.2 2018-01-17 13:50:56 350 repeatmasker_wrapper_output_stats2
131296 1 6472 output_meme [{"type":"html","id":"156f1212d2e33df6","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/156f1212d2e33df6/display?preview=True"},{"type":"txt","id":"9291e4475f23e81b","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/9291e4475f23e81b/display?preview=True"}] {"code":"OK"} {"input1":"{\"values\": [{\"src\": \"hda\", \"id\": 26910}]}","dbkey":"\"sacCer3_cegr\"","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","input1Xidentifier":"\"data_MP_mode_f0u0d80_on_data_26.gff\"","non_commercial_use":"\"true\"","options_type":"{\"distance\": \"0.001\", \"bfile\": null, \"options_type_selector\": \"advanced\", \"maxiter\": \"50\", \"mod_type\": {\"motif_occurrence_type\": {\"motif_occurrence_type_selector\": \"default\", \"current_case\": 0}, \"mod_type_selector\": \"zoops\", \"current_case\": 1}, \"nmotifs\": \"3\", \"wnsites\": \"0.8\", \"pspfile\": null, \"branching_type\": {\"current_case\": 0, \"branching_type_selector\": \"no_x_branch\"}, \"current_case\": 1, \"motif_width_type\": {\"motif_width_type_selector\": \"range\", \"maxw\": \"50\", \"current_case__\": 1, \"minw\": \"8\"}, \"motif_trim_type\": {\"wg\": \"11\", \"motif_trim_type_selector\": \"trim\", \"noendgaps\": \"false\", \"ws\": \"1\", \"current_case\": 1}, \"alphabet_type\": {\"prior_type\": {\"plib\": null, \"prior_b\": \"0.01\", \"__current_case\": 0, \"prior_type_selector\": \"dirichlet\"}, \"current_case__\": 1, \"revcomp\": \"true\", \"spmap_type\": {\"spfuzz\": \"0.5\", \"spmap_type_selector\": \"uni\", \"current_case__\": 0}, \"pal\": \"false\", \"alphabet_type_selector\": \"dna\"}, \"evt\": \"0.0001\", \"sf\": \"Galaxy FASTA Input\"}","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{"motifCount":3}] f85690fd6635fb3d toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.2.0 2018-01-17 13:52:16 350 meme_meme_output_stats
131298 1 6472 output_fimo [{"type":"gff","id":"494f37cff5f08a27","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/494f37cff5f08a27/display?preview=True"},{"type":"gff","id":"3028ef4a56bac4f1","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/3028ef4a56bac4f1/display?preview=True"},{"type":"gff","id":"79699228892a86f6","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/79699228892a86f6/display?preview=True"},{"type":"cisml","id":"ae626d3394765cbc","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/ae626d3394765cbc/display?preview=True"}] {"code":"OK"} {"workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","input_databaseXidentifier":"\"data_MP_mode_f0u0d80_on_data_26.gff\"","dbkey":"\"sacCer3_cegr\"","input_motifsXidentifier":"\"data_MP_mode_f0u0d80_on_data_26.gff\"","input_motifs":"{\"values\": [{\"src\": \"hda\", \"id\": 26915}]}","non_commercial_use":"\"true\"","options_type":"{\"prior_dist_cond\": {\"prior_dist_selector\": \"no\", \"current_case\": 0}, \"qv_thresh\": \"false\", \"psp_cond\": {\"current_case\": 0, \"psp_selector\": \"no\"}, \"options_type_selector\": \"advanced\", \"no_qvalue\": \"true\", \"output_separate_motifs\": \"yes\", \"parse_genomic_coord_cond\": {\"remove_duplicate_coords\": \"yes\", \"current_case\": 0, \"parse_genomic_coord\": \"yes\"}, \"motifs_cond\": {\"motifs_selector\": \"yes\", \"current_case\": 0}, \"bgfile_type\": {\"bgfile_type_selector\": \"default\", \"current_case__\": 1}, \"norc\": \"false\", \"max_strand\": \"false\", \"thresh\": \"0.0001\", \"current_case\": 1, \"max_stored_scores\": \"100000\", \"alpha\": \"1.0\", \"motif_pseudo\": \"0.1\"}","fasta_type":"{\"input_database\": {\"values\": [{\"src\": \"hda\", \"id\": 26904}]}, \"fasta_type_selector\": \"history\", \"__current_case\": 1}","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{},{},{},{}] a4b04edad39fbad2 toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0 2018-01-17 13:53:23 350 meme_fimo_output_stats
131305 1 6472 output_fourColorPlot [{"type":"png","id":"6f72e97a60c1137b","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/6f72e97a60c1137b/display?preview=True"},{"type":"png","id":"c7039a4b5a5f7971","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/c7039a4b5a5f7971/display?preview=True"},{"type":"png","id":"3f70e826f038a87f","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/3f70e826f038a87f/display?preview=True"}] {"code":"OK"} {"a_select_color_cond":"{\"a_rgb\": \"254,25,24\", \"a_select_color\": \"a_rgb\", \"current_case__\": 1}","c_select_color_cond":"{\"c_rgb\": \"43,49,246\", \"c_select_color\": \"c_rgb\", \"current_case\": 1}","inputXidentifier":"\"MOTIF3.gff\"","g_select_color_cond":"{\"g_select_color\": \"g_rgb\", \"g_rgb\": \"252,252,80\", \"__current_case\": 1}","n_select_color_cond":"{\"n_select_color\": \"n_rgb\", \"current_case\": 1, \"n_rgb\": \"128,128,128\"}","t_select_color_cond":"{\"t_select_color\": \"t_rgb\", \"t_rgb\": \"50,204,60\", \"current_case\": 1}","dbkey":"\"sacCer3_cegr\"","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","input":"{\"values\": [{\"src\": \"hda\", \"id\": 26993}]}","pixel_height":"\"2\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\"","pixel_width":"\"2\""} [{},{},{}] c0d76bc7e1e8aa3f toolshed.g2.bx.psu.edu/repos/iuc/fasta_nucleotide_color_plot/fasta_nucleotide_color_plot/1.0.1 2018-01-17 13:55:50 350 fasta_nucleotide_color_plot_output_stats
131308 1 6472 output_tagPileup [{"type":"tabular","id":"6957ae2e8334ce9b","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/6957ae2e8334ce9b/display?preview=True"},{"type":"tabular","id":"880528edd54a8323","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/880528edd54a8323/display?preview=True"},{"type":"tabular","id":"c3807dbcf3d77693","uri":"http://chipexo-gw.aci.ics.psu.edu:8080/datasets/c3807dbcf3d77693/display?preview=True"}] {"code":"OK"} {"input2":"{\"values\": [{\"src\": \"hda\", \"id\": 26994}]}","input2Xidentifier":"\"MOTIF1.gff\"","input1":"{\"values\": [{\"src\": \"hda\", \"id\": 26775}]}","bin_size":"\"1\"","output_heatmap":"\"true\"","tag_shift":"\"0\"","workflow_invocation_uuid":"\"d6c2a30afbb511e7b4d8005056b99835\"","proper_pe":"\"false\"","reads":"\"0\"","composite_smoothing_window":"\"0\"","dbkey":"\"sacCer3_cegr\"","tags_equal":"\"false\"","combine_strands":"\"0\"","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{},{},{}] 1dc8dee747cb1130 toolshed.g2.bx.psu.edu/repos/iuc/tag_pileup_frequency/tag_pileup_frequency/1.0.1 2018-01-17 13:56:05 350 tag_pileup_frequency_output_stats
183308 1 9151 output_bwaMem [{"type":"bam","id":"804892944f6df20e","uri":"http://chipexo-gw.aci.ics.psu.edu/datasets/804892944f6df20e/display?preview=True"}] {"code":"OK"} {"workflow_invocation_uuid":"\"82d2b3221b2511e89ca9005056b99835\"","dbkey":"\"sacCer3_cegr\"","rg":"{\"rg_selector\": \"do_not_set\", \"current_case__\": 3}","fastq_input":"{\"current_case\": 1, \"fastq_input_selector\": \"single\", \"fastq_input1\": {\"values\": [{\"src\": \"hda\", \"id\": 229364}]}}","analysis_type":"{\"analysis_type_selector\": \"full\", \"algorithmic_options\": {\"algorithmic_options_selector\": \"do_not_set\", \"__current_case\": 1}, \"io_options\": {\"a\": \"false\", \"C\": \"false\", \"io_options_selector\": \"set\", \"h\": \"5\", \"M\": \"true\", \"q\": \"false\", \"five\": \"false\", \"T\": \"30\", \"current_case\": 0, \"V\": \"false\", \"Y\": \"false\"}, \"current_case\": 4, \"scoring_options\": {\"scoring_options_selector\": \"do_not_set\", \"current_case__\": 1}}","reference_source":"{\"ref_file\": \"sacCer3_cegr\", \"reference_source_selector\": \"cached\", \"current_case__\": 0}","chromInfo":"\"/gpfs/group/bfp2/pughlab/galaxy/tool-data/sacCer3_cegr/len/sacCer3_cegr.len\""} [{"totalReads":6499854.0,"dedupUniquelyMappedReads":5414128.0,"uniquelyMappedReads":5414128.0,"mappedReads":5414134.0}] b9d42b1967352e2f toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2018-02-26 13:51:32 350 bwa_mem_output_stats_single

scroll to the right to view the entire table :tada:

id version alignment_id category datasets note parameters statistics step_id tool date user_id step
149761 3 7318 multiGPS {"code":"OK"} [{"multiGPS":12}] 001 2018-01-31 09:46:07 277 multiGPS
143360 1 6857 significanceTester {"code":"OK"} [{"sigPeakPairs":0}] 002 2018-01-29 01:05:13 277 significanceTester
137216 5 6509 stamp {"code":"OK"} [{"stamp":"No"}] 004 2018-01-28 17:39:09 277 stamp
184038 1 8118 nucleosomeEnrichmentProfiler {"code":"OK"} [{"nucleosomeEnrichment":"2.30"}] 005 2018-02-28 14:33:24 277 nucleosomeEnrichmentProfiler
143622 1 6898 pointEnrichmentTester {"code":"OK"} [{"enrichedSegments":"Telomere tRNA"}] 006 2018-01-29 02:29:34 277 pointEnrichmentTester
184108 1 8274 tableLookup {"code":"OK"} [{"go":"cellular response to DNA damage stimulus","exprsLevel":"0.38","polIILevel":"0.48"}] 007 2018-02-28 14:46:13 277 tableLookup