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annotate guppy_basecaller.xml @ 6:78d793671a9e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy commit eb65a3ba03e7c4470f9ccc253c68a1a822bd46f4
author artbio
date Sun, 10 Dec 2023 15:06:44 +0000
parents dd0cccf3a62f
children 6977341bd461
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78d793671a9e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy commit eb65a3ba03e7c4470f9ccc253c68a1a822bd46f4
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1 <tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.2.2" python_template_version="3.8">
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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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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
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21 && cat out/*.fastq | awk '{ if (NR%4 == 2) {gsub(/U/,"T",$1); print $1} else print }' > $output_fastq
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22 ]]></command>
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23 <inputs>
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24 <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>
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25 <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
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26 </inputs>
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27 <outputs>
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28 <data name="output_fastq" format="fastqsanger" />
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29 </outputs>
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30 <help><![CDATA[
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31 A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,
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32 and a configuration in the form of a tar file.
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34 You can find configurations at https://github.com/nanoporetech/rerio,
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35 and in particular the directory `nanoporetech/rerio/basecall_models`.
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37 Each file there contains a URL you can download to use, for example
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38 https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_rna2_r941_min_flipflop_v001
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39 points to 'https://nanoporetech.box.com/shared/static/84e1jeudx8lr8ay7e9u1ebnvx3bk2kjf.tgz'
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41 When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?).
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43 The results should be fastq files.
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45 ------
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47 guppy_basecaller --help
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48 : 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 **Usage**::
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52 With config file::
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54 guppy_basecaller -i <input path> -s <save path> -c <config file> [options]
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56 With flowcell and kit name::
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58 guppy_basecaller -i <input path> -s <save path> --flowcell <flowcell name>
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59 --kit <kit name>
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61 List supported flowcells and kits::
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63 guppy_basecaller --print_workflows
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65 Use server for basecalling::
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67 guppy_basecaller -i <input path> -s <save path> -c <config file>
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68 --port <server address> [options]
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71 **Command line parameters**::
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73 --trim_threshold arg Threshold above which data will be trimmed
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74 (in standard deviations of current level
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75 distribution).
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76 --trim_min_events arg Adapter trimmer minimum stride intervals
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77 after stall that must be seen.
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78 --max_search_len arg Maximum number of samples to search through
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79 for the stall
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80 --override_scaling Manually provide scaling parameters rather
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81 than estimating them from each read.
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82 --scaling_med arg Median current value to use for manual
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83 scaling.
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84 --scaling_mad arg Median absolute deviation to use for manual
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85 scaling.
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diff changeset
86 --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
87 (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
88 --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
89 detection
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
90 --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
91 --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
92 --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
93 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
94 --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
95 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
96 --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
97 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
98 (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
99 --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
100 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
101 30.0)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
102 --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
103 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
104 30)
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
105 --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
106 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
107 --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
108 adapter scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
109 --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
110 scaler
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
111 --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
112 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
113 --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
114 scaling.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
115 -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
116 -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
117 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
118 -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
parents:
diff changeset
119 '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
120 --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
121 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
122 --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
123 --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
124 --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
125 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
126 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
127 --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
128 for each medium priority chunk.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
129 --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
130 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
131 --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
parents:
diff changeset
132 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
133 --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
134 --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
parents:
diff changeset
135 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
136 --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
137 --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
138 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
139 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
140 --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
141 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
142 --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
143 --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
144 --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
145 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
146 --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
147 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
148 --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
149 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
150 --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
parents:
diff changeset
151 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
152 --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
153 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
154 --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
155 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
156 --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
157 --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
158 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
159 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
160 --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
161 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
162 --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
163 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
164 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
165 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
166 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
167 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
168 --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
169 --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
170 --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
parents:
diff changeset
171 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
172 --end_gap1 arg Gap penalty for aligning after 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
173 reference.
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artbio
parents:
diff changeset
174 --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
175 reference.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
parents:
diff changeset
176 --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
177 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
178 --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
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diff changeset
179 --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
180 --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
181 --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
182 --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
parents:
diff changeset
183 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
184 --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
185 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
186 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
parents:
diff changeset
187 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
188 --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
189 --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
190 --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
191 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
192 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
193 --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
194 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
195 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
196 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
197 --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
198 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
199 --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
200 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
201 --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
202 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
203 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
204 --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
205 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
206 --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
207 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
208 --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
209 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
210 --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
211 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
212 --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
213 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
214 --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
215 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
216 --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
217 --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
218 --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
219 -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
220 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
221 --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
222 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
223 --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
224 --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
225 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
226 --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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diff changeset
227 --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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228 -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
229 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
230 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
231 --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
232 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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233 --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
234 -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
235 --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
236 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
237 -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
238 -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
239 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
240 -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
241 --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
242 --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
243 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
244 --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
245 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
246 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
247 --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
248 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
249 -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
250 --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
251 --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
252 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
253 --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
254 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
255 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
256 --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
257 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
258 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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diff changeset
259 part of the output filenames.
fb42dde97559 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty"
artbio
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260 --nested_output_folder If flagged output fastq files will be
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261 written to a nested folder structure, based
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262 on: protocol_group/sample/protocol/qscore_p
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263 ass_fail/barcode_arrangement/
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264 -h [ --help ] produce help message
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265 -v [ --version ] print version number
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266 -c [ --config ] arg Config file to use
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267 -d [ --data_path ] arg Path to use for loading any data files the
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268 application requires.
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269
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270
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271 ------
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272 ]]></help>
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273 </tool>