Mercurial > repos > jdv > albacore
changeset 2:b658298e65d8 draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
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--- a/albacore_1D.xml Wed Sep 06 12:12:52 2017 -0400 +++ b/albacore_1D.xml Fri Sep 08 10:14:40 2017 -0400 @@ -28,7 +28,7 @@ <inputs> - <param name="input" type="data" format="fast5_archive" label="Input reads" /> + <param name="input" type="data" format="fast5.tar" label="Input reads" /> <param name="out_format" type="select" label="Output format"> <option value="fastq" selected="true">fastq</option> <option value="fast5">fast5</option> @@ -44,7 +44,7 @@ <data name="output" format="fastq" label="${tool.name} on ${on_string} (reads)"> <filter>demux is False</filter> <change_format> - <when input="out_format" value="fast5" format="fast5_archive" /> + <when input="out_format" value="fast5" format="fast5.tar.gz" /> </change_format> </data> <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string} (reads)"> @@ -53,7 +53,7 @@ </collection> <collection type="list" name="output_collection_fast5" label="${tool.name} on ${on_string} (reads)"> <filter>demux is True and out_format == 'fast5'</filter> - <discover_datasets pattern="(?P<name>.*)" directory="final" format="fast5_archive" /> + <discover_datasets pattern="(?P<name>.*)" directory="final" format="fast5.tar.gz" /> </collection> <data name="table" format="tabular" from_work_dir="out_dir/sequencing_summary.txt" label="${tool.name} on ${on_string} (table)" /> @@ -63,7 +63,7 @@ <tests> <test> - <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" /> + <param name="input" value="test_data.fast5.tar.gz" ftype="fast5.tar.gz" /> <output name="output" file="test_data.fastq" compare="diff" /> </test> </tests>
--- a/albacore_denoise.xml Wed Sep 06 12:12:52 2017 -0400 +++ b/albacore_denoise.xml Fri Sep 08 10:14:40 2017 -0400 @@ -46,7 +46,7 @@ <inputs> - <param name="inputs" type="data_collection" collection_type="list" format="fast5_archive" label="Input reads" multiple="true" /> + <param name="inputs" type="data_collection" collection_type="list" format="fast5.tar" label="Input reads" multiple="true" /> <param name="table" type="data" format="tabular" label="Read table" /> <conditional name="filter"> <param name="type" type="select" label="Filtering type"> @@ -70,7 +70,7 @@ <outputs> <collection type="list" name="outputs" label="${tool.name} on ${on_string} (reads)"> - <discover_datasets pattern="(?P<name>.*)\.fast5\.tar\.gz$" directory="outputs" format="fast5_archive" /> + <discover_datasets pattern="(?P<name>.*)\.fast5\.tar\.gz$" directory="outputs" format="fast5.tar.gz" /> </collection> <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" /> @@ -79,14 +79,8 @@ <!-- ***************************************************************** --> - <!-- <tests> - <test> - <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" /> - <output name="output" file="test_data.fastq" compare="diff" /> - </test> </tests> - --> <!-- ***************************************************************** -->
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out_dir/configuration.cfg Fri Sep 08 10:14:40 2017 -0400 @@ -0,0 +1,57 @@ +[pipeline] +basecall_type = linear +log_summaries = false +log_all_intermodule_messages = false +desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_basecall_barcode_1d.jsn + +[data_trimmer] +ev_window = 20 +ev_threshold = 5 +min_events = 3 +delta = 2 + +[event_detector] +window1 = 4 +window2 = 8 +threshold1 = 1.5 +threshold2 = 9.0 +peak_height = 0.2 +min_events = 1000 +trim_front = 0 + +[basecaller] +model = template_r9.5_450bps_5mer.jsn +min_events = 100 +max_events = 1000 +overlap = 50 +min_quality = -100.0 +min_prob = 1e-5 +simple_decoding = 1 +model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned + +[call_handler] +record_base = read +qscore_adjuster_intercept = -4.5 +qscore_adjuster_slope = 3.0 + +[barcode_detector] +arrangements_files = barcode_arrs_pcr96.cfg barcode_arrs_nb.cfg barcode_arrs_rbk.cfg barcode_arrs_lwb.cfg barcode_arrs_rlb.cfg barcode_arrs_rab.cfg +score_matrix = 4x4_mismatch_matrix.txt +start_gap1 = 40 +end_gap1 = 40 +open_gap1 = 40 +extend_gap1 = 40 +start_gap2 = 40 +end_gap2 = 40 +open_gap2 = 160 +extend_gap2 = 160 +min_score = 60.0 +front_window_size = 150 +rear_window_size = 150 + +[fastq] +header = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} +header_with_barcoding = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id} +batch_file_name = fastq_runid_{run_id}_{batch_counter}.fastq +single_file_name = {read_id}.fastq +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out_dir/pipeline.log Fri Sep 08 10:14:40 2017 -0400 @@ -0,0 +1,21 @@ +2017-09-08 09:12:50,286 ONT Albacore Sequencing Pipeline Software (version 1.2.6) +2017-09-08 09:12:50,286 Debug level is 0 +2017-09-08 09:12:50,292 Selected config file /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/r95_450bps_linear.cfg to match flowcell FLO-MIN107 and kit SQK-LSK108 +2017-09-08 09:12:50,292 Loaded barcoding config from /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/barcoding.cfg +2017-09-08 09:12:51,304 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5". +2017-09-08 09:12:51,456 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5". +2017-09-08 09:12:51,550 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5". +2017-09-08 09:12:51,644 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5". +2017-09-08 09:12:51,671 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5". +2017-09-08 09:12:51,786 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5". +2017-09-08 09:12:51,840 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5". +2017-09-08 09:12:52,070 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5". +2017-09-08 09:12:52,124 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5". +2017-09-08 09:12:52,395 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5". +2017-09-08 09:12:52,450 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5". +2017-09-08 09:12:52,656 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5". +2017-09-08 09:12:52,681 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5". +2017-09-08 09:12:52,819 Submitting file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5". +2017-09-08 09:12:52,873 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5". +2017-09-08 09:12:53,126 Finished processing file "macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5". +2017-09-08 09:12:53,128 Done.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out_dir/sequencing_summary.txt Fri Sep 08 10:14:40 2017 -0400 @@ -0,0 +1,9 @@ +filename read_id run_id channel start_time duration num_events template_start num_events_template template_duration num_called_template sequence_length_template mean_qscore_template strand_score_template barcode_arrangement barcode_score barcode_full_arrangement front_score rear_score front_begin_index front_foundseq_length rear_end_index rear_foundseq_length kit variant +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12068_ch_399_strand.fast5 3030a28d-1f16-4086-9ba1-ff31a97f434d d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5196.22842 1.10525 861 0.05129 861 1.05395 861 441 6.087 -0.0015 unclassified 37.230770111083984 NB09_var1 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12091_ch_399_strand.fast5 86fd3e14-b5ee-4453-98fa-084d75821456 d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5208.88562 1.84645 1417 0.09329 1417 1.75315 1417 793 6.096 -0.0017 unclassified 39.43589782714844 NB09_var2 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12153_ch_399_strand.fast5 2dd21811-c9af-4c4a-aaa0-4fd1f605abf8 d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5224.53552 1.14675 910 0.04997 910 1.09678 910 512 6.447 -0.0013 unclassified 33.28205108642578 NB08_var1 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12175_ch_399_strand.fast5 28daae22-d0dc-4fee-8453-3a2178b331c8 d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5230.13961 2.28967 1728 0.11604 1728 2.17364 1728 964 6.992 -0.001 unclassified 34.377357482910156 LWB09_var2 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12081_ch_399_strand.fast5 15bdfe23-0646-4c89-b523-185bc14c3a2a d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5202.95983 2.90405 2423 0.01726 2423 2.88679 2423 1276 5.486 -0.0018 unclassified 35.8983039855957 BC24_var2 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12113_ch_399_strand.fast5 310f7b48-a3e0-4cdc-b396-09f4b86081dd d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5216.31192 1.84894 1486 0.0 1486 1.84894 1486 821 6.153 -0.0018 unclassified 35.66101837158203 BC15_var1 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12085_ch_399_strand.fast5 921ea44a-1215-4f98-9f38-bf36b1bdf69c d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5206.51394 1.57155 1271 0.0 1271 1.57155 1271 634 6.138 -0.0011 unclassified 29.743589401245117 NB04_var1 -inf -inf -1 0 -1 0 n/a n/a +macs_MacBook_local_20170809_FAH11850_MN21227_sequencing_run_AIV_run_1_84332_read_12103_ch_399_strand.fast5 aabaf035-7aa8-439b-8773-523c69a350ca d28f9f1c34b8f7416c367df1e0c4a864ba830c9c 1 5212.72327 1.70734 1427 0.0 1427 1.70734 1427 824 5.971 -0.0014 unclassified 33.01960754394531 RLB05 -inf -inf -1 0 -1 0 n/a n/a
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