Mercurial > repos > jdv > albacore

annotate out_dir/configuration.cfg @ 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
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3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
parents:
diff changeset
1 [pipeline]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
2 basecall_type = linear
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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3 min_qscore_1d = 7.0
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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4 desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_raw_basecall_1d.jsn
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
5 log_intermodule_messages = False
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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6
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
7 [data_trimmer]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
8 ev_window = 20
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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9 ev_threshold = 5
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
10 min_events = 3
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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11 delta = 2
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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12 chunk_size_out = 0 # Use a nonzero value to chunk output
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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13
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
14 [basecaller]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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15 model = template_r9.5_450bps_5mer_raw.jsn
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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16 implementation = auto
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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17 min_events = 100
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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18 max_events = 10000
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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19 overlap = 50
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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diff changeset
20 min_quality = -10.0
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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21 min_prob = 1e-5
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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22 simple_decoding = 1
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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23 homopolymer_correct = 0
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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24 model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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26 [call_handler]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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27 record_base = read
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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28 qscore_adjuster_intercept = 1.5
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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29 qscore_adjuster_slope = 1.5
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
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30
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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31 [barcode_detector]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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32
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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33 [fastq]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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34 identifier = {read_id}
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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35 header = {identifier} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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36 header_with_barcoding = {identifier} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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37 batch_file_name = fastq_runid_{run_id}_{batch_counter}.{extension}
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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38 single_file_name = {read_id}.{extension}
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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39 all_file_name = fastq_runid_{run_id}.fastq
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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40
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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41 [fast5]
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
jdv
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42 basecall_columns = mean,start,stdv,length,model_state,move,p_model_state,weights
3dfde840119e planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
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