Mercurial > repos > artbio > guppy_basecaller

annotate guppy_basecaller.xml @ 1:93b6cbff5ea4 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit d9a24dd18eb10e9b47aa5ad4414b8725df6d0eb3"
author artbio
date Thu, 19 Nov 2020 00:03:03 +0000
parents fb42dde97559
children cfc7ff08ad20
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fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
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1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.4" python_template_version="3.5">
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2 <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
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3 <requirements>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
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7 #for $file in $infiles:
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8 ln -s $file ${file.element_identifier}.fast5 &&
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9 #end for
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10 tar xf $config &&
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11 guppy_basecaller -i .
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12 --save_path out
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13 --data_path .
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14 --config *.cfg
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15 --num_callers 4
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16 --records_per_fastq 0
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17 --cpu_threads_per_caller \${GALAXY_SLOTS:-2}
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18 --disable_pings
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19 --qscore_filtering
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20 ### --calib_detect
0
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21 ]]></command>
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22 <inputs>
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23 <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
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24 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
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25 </inputs>
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26 <outputs>
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27 <data name="guppy_result" format="fastq">
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28 <discover_datasets directory="out/PASS" ext="fastq" pattern=".+\.fastq" visible="true"/>
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29 </data>
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30 </outputs>
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31 <help><![CDATA[
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32 A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
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33 and a configuration in the form of a tar file.
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35 You can find configurations at https://github.com/nanoporetech/rerio,
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36 and in particular the directory https://github.com/nanoporetech/rerio/basecall_models.
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fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
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38 Each file there contains a URL you can download to use, for example
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39 https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_rna2_r941_min_flipflop_v001
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40 points to 'https://nanoporetech.box.com/shared/static/84e1jeudx8lr8ay7e9u1ebnvx3bk2kjf.tgz'
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fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
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42 When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?).
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44 The results should be fastq files.
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46 ------
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48 guppy_basecaller --help
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49 : Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.6.1+249406c, client-server API version 1.1.0
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50
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51 **Usage**::
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52
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53 With config file::
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55 guppy_basecaller -i <input path> -s <save path> -c <config file> [options]
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57 With flowcell and kit name::
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59 guppy_basecaller -i <input path> -s <save path> --flowcell <flowcell name>
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60 --kit <kit name>
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62 List supported flowcells and kits::
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64 guppy_basecaller --print_workflows
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66 Use server for basecalling::
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68 guppy_basecaller -i <input path> -s <save path> -c <config file>
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69 --port <server address> [options]
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72 **Command line parameters**::
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74 --trim_threshold arg Threshold above which data will be trimmed
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75 (in standard deviations of current level
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76 distribution).
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77 --trim_min_events arg Adapter trimmer minimum stride intervals
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78 after stall that must be seen.
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79 --max_search_len arg Maximum number of samples to search through
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80 for the stall
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81 --override_scaling Manually provide scaling parameters rather
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82 than estimating them from each read.
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83 --scaling_med arg Median current value to use for manual
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84 scaling.
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85 --scaling_mad arg Median absolute deviation to use for manual
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86 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
87 --trim_strategy arg Trimming strategy to apply: 'dna' or 'rna'
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
88 (or 'none' to disable trimming)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
89 --dmean_win_size arg Window size for coarse stall event
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
90 detection
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
91 --dmean_threshold arg Threhold for coarse stall event detection
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
92 --jump_threshold arg Threshold level for rna stall detection
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
93 --pt_scaling Enable polyT/adapter max detection for read
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
94 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
95 --pt_median_offset arg Set polyT median offset for setting read
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
96 scaling median (default 2.5)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
97 --adapter_pt_range_scale arg Set polyT/adapter range scale for setting
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
98 read scaling median absolute deviation
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
99 (default 5.2)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
100 --pt_required_adapter_drop arg Set minimum required current drop from
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
101 adapter max to polyT detection. (default
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
102 30.0)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
103 --pt_minimum_read_start_index arg Set minimum index for read start sample
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
104 required to attempt polyT scaling. (default
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
105 30)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
106 --as_model_file arg Path to JSON model file for adapter
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
107 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
108 --as_gpu_runners_per_device arg Number of runners per GPU device for
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
109 adapter scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
110 --as_cpu_threads_per_scaler arg Number of CPU worker threads per adapter
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
111 scaler
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
112 --as_reads_per_runner arg Maximum reads per runner for adapter
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
113 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
114 --as_num_scalers arg Number of parallel scalers for adapter
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
115 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
116 -m [ --model_file ] arg Path to JSON model file.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
117 -k [ --kernel_path ] arg Path to GPU kernel files location (only
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
118 needed if builtin_scripts is false).
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
119 -x [ --device ] arg Specify basecalling device: 'auto', or
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
120 'cuda:<device_id>'.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
121 --builtin_scripts arg Whether to use GPU kernels that were
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
122 included at compile-time.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
123 --chunk_size arg Stride intervals per chunk.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
124 --chunks_per_runner arg Maximum chunks per runner.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
125 --chunks_per_caller arg Soft limit on number of chunks in each
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
126 caller's queue. New reads will not be
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
127 queued while this is exceeded.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
128 --high_priority_threshold arg Number of high priority chunks to process
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
129 for each medium priority chunk.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
130 --medium_priority_threshold arg Number of medium priority chunks to process
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
131 for each low priority chunk.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
132 --overlap arg Overlap between chunks (in stride
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
133 intervals).
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
134 --gpu_runners_per_device arg Number of runners per GPU device.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
135 --cpu_threads_per_caller arg Number of CPU worker threads per
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
136 basecaller.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
137 --num_callers arg Number of parallel basecallers to create.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
138 --post_out Return full posterior matrix in output
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
139 fast5 file and/or called read message from
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
140 server.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
141 --stay_penalty arg Scaling factor to apply to stay probability
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
142 calculation during transducer decode.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
143 --qscore_offset arg Qscore calibration offset.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
144 --qscore_scale arg Qscore calibration scale factor.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
145 --temp_weight arg Temperature adjustment for weight matrix in
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
146 softmax layer of RNN.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
147 --temp_bias arg Temperature adjustment for bias vector in
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
148 softmax layer of RNN.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
149 --qscore_filtering Enable filtering of reads into PASS/FAIL
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
150 folders based on min qscore.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
151 --min_qscore arg Minimum acceptable qscore for a read to be
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
152 filtered into the PASS folder
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
153 --reverse_sequence arg Reverse the called sequence (for RNA
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
154 sequencing).
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
155 --u_substitution arg Substitute 'U' for 'T' in the called
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
156 sequence (for RNA sequencing).
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
157 --log_speed_frequency arg How often to print out basecalling speed.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
158 --barcode_kits arg Space separated list of barcoding kit(s) or
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
159 expansion kit(s) to detect against. Must be
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
160 in double quotes.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
161 --trim_barcodes Trim the barcodes from the output sequences
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
162 in the FastQ files.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
163 --num_extra_bases_trim arg How vigorous to be in trimming the barcode.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
164 Default is 0 i.e. the length of the
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
165 detected barcode. A positive integer means
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
166 extra bases will be trimmed, a negative
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
167 number is how many fewer bases (less
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
168 vigorous) will be trimmed.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
169 --arrangements_files arg Files containing arrangements.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
170 --score_matrix_filename arg File containing mismatch score matrix.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
171 --start_gap1 arg Gap penalty for aligning before the
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
172 reference.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
173 --end_gap1 arg Gap penalty for aligning after the
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artbio
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diff changeset
174 reference.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
175 --open_gap1 arg Penalty for opening a new gap in the
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
176 reference.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
177 --extend_gap1 arg Penalty for extending a gap in the
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
178 reference.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
179 --start_gap2 arg Gap penalty for aligning before the query.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
180 --end_gap2 arg Gap penalty for aligning after the query.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
181 --open_gap2 arg Penalty for opening a new gap in the query.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
182 --extend_gap2 arg Penalty for extending a gap in the query.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
183 --min_score arg Minimum score to consider a valid
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
184 alignment.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
185 --min_score_rear_override arg Minimum score to consider a valid alignment
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
186 for the rear barcode only (and min_score
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
187 will then be used for the front only when
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
188 this is set).
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
189 --front_window_size arg Window size for the beginning barcode.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
190 --rear_window_size arg Window size for the ending barcode.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
191 --require_barcodes_both_ends Reads will only be classified if there is a
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
192 barcode above the min_score at both ends of
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
193 the read.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
194 --allow_inferior_barcodes Reads will still be classified even if both
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
195 the barcodes at the front and rear (if
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
196 applicable) were not the best scoring
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
197 barcodes above the min_score.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
198 --detect_mid_strand_barcodes Search for barcodes through the entire
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
199 length of the read.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
200 --min_score_mid_barcodes arg Minimum score for a barcode to be detected
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
201 in the middle of a read.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
202 --num_barcoding_buffers arg Number of GPU memory buffers to allocate to
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
203 perform barcoding into. Controls level of
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
204 parallelism on GPU for barcoding.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
205 --num_barcode_threads arg Number of worker threads to use for
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
206 barcoding.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
207 --calib_detect Enable calibration strand detection and
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
208 filtering.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
209 --calib_reference arg Reference FASTA file containing calibration
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
210 strand.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
211 --calib_min_sequence_length arg Minimum sequence length for reads to be
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
212 considered candidate calibration strands.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
213 --calib_max_sequence_length arg Maximum sequence length for reads to be
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
214 considered candidate calibration strands.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
215 --calib_min_coverage arg Minimum reference coverage to pass
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
216 calibration strand detection.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
217 --print_workflows Output available workflows.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
218 --flowcell arg Flowcell to find a configuration for
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
219 --kit arg Kit to find a configuration for
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
220 -z [ --quiet ] Quiet mode. Nothing will be output to
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
221 STDOUT if this option is set.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
222 --trace_categories_logs arg Enable trace logs - list of strings with
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
223 the desired names.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
224 --verbose_logs Enable verbose logs.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
225 --disable_pings Disable the transmission of telemetry
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
226 pings.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
227 --ping_url arg URL to send pings to
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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228 --ping_segment_duration arg Duration in minutes of each ping segment.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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229 -q [ --records_per_fastq ] arg Maximum number of records per fastq file, 0
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
230 means use a single file (per worker, per
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
231 run id).
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
232 --read_batch_size arg Maximum batch size, in reads, for grouping
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
233 input files.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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234 --compress_fastq Compress fastq output files with gzip.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
235 -i [ --input_path ] arg Path to input fast5 files.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
236 --input_file_list arg Optional file containing list of input
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
237 fast5 files to process from the input_path.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
238 -s [ --save_path ] arg Path to save fastq files.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
239 -l [ --read_id_list ] arg File containing list of read ids to filter
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
240 to
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
241 -r [ --recursive ] Search for input files recursively.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
242 --fast5_out Choice of whether to do fast5 output.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
243 --resume Resume a previous basecall run using the
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
244 same output folder.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
245 --progress_stats_frequency arg Frequency in seconds in which to report
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
246 progress statistics, if supplied will
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
247 replace the default progress display.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
248 --max_block_size arg Maximum block size (in events) of basecall
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
249 messages to server.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
250 -p [ --port ] arg Port for basecalling service.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
251 --barcoding_config_file arg Configuration file to use for barcoding.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
252 --num_barcode_threads arg Number of worker threads to use for
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
253 barcoding.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
254 --disable_events Disable the transmission of event tables
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
255 when receiving reads back from the basecall
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
256 server.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
257 --client_id arg Optional unique identifier (non-negative
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
258 integer) for this instance of the Guppy
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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diff changeset
259 Client Basecaller, if supplied will form
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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260 part of the output filenames.
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261 --nested_output_folder If flagged output fastq files will be
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262 written to a nested folder structure, based
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263 on: protocol_group/sample/protocol/qscore_p
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264 ass_fail/barcode_arrangement/
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265 -h [ --help ] produce help message
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266 -v [ --version ] print version number
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267 -c [ --config ] arg Config file to use
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268 -d [ --data_path ] arg Path to use for loading any data files the
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269 application requires.
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270
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271
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272 ------
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273 ]]></help>
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274 </tool>