| Next changeset 1:93b6cbff5ea4 (2020-11-19) |
|
Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/guppy commit ebd2091cbe5b34821c7c1192949dbec5f4d2eb03-dirty" |
|
added:
guppy_basecaller.xml |
| b |
| diff -r 000000000000 -r fb42dde97559 guppy_basecaller.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/guppy_basecaller.xml Wed Nov 18 23:26:35 2020 +0000 |
| [ |
| b'@@ -0,0 +1,274 @@\n+<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.4" python_template_version="3.5">\n+ <description>A simple wrapper for guppy basecaller that depends on configuration files</description>\n+ <requirements>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ #for $file in $infiles:\n+ ln -s $file ${file.element_identifier}.fast5 &&\n+ #end for\n+ tar xf $config &&\n+ guppy_basecaller -i .\n+ --save_path out\n+ --data_path .\n+ --config *.cfg\n+ --num_callers 4\n+ --records_per_fastq 0\n+ --cpu_threads_per_caller \\${GALAXY_SLOTS:-2}\n+ --disable_pings\n+ --qscore_filtering\n+ --calib_detect\n+ ]]></command>\n+ <inputs>\n+ <param name="infiles" type="data_collection" format="h5" label="Fast5 input (datatype h5)" multiple="true"/>\n+ <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>\n+ </inputs>\n+ <outputs>\n+ <data name="guppy_result" format="fastq">\n+ <discover_datasets directory="out/PASS" ext="fastq" pattern=".+\\.fastq" visible="true"/>\n+ </data>\n+ </outputs>\n+ <help><![CDATA[\n+ A wrapper for guppy basecaller. This expects two type of inputs: a collection of fast5 files,\n+ and a configuration in the form of a tar file.\n+\n+ You can find configurations at https://github.com/nanoporetech/rerio,\n+ and in particular the directory https://github.com/nanoporetech/rerio/basecall_models.\n+\n+ Each file there contains a URL you can download to use, for example\n+ https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_rna2_r941_min_flipflop_v001\n+ points to \'https://nanoporetech.box.com/shared/static/84e1jeudx8lr8ay7e9u1ebnvx3bk2kjf.tgz\'\n+\n+ When uploading these .tgz files take care to set the format to \'tar\' (galaxy doesn\'t autodetect this?).\n+\n+ The results should be fastq files.\n+\n+------\n+\n+guppy_basecaller --help\n+: Guppy Basecalling Software, (C) Oxford Nanopore Technologies, Limited. Version 3.6.1+249406c, client-server API version 1.1.0\n+\n+**Usage**::\n+\n+With config file::\n+\n+ guppy_basecaller -i <input path> -s <save path> -c <config file> [options]\n+\n+With flowcell and kit name::\n+\n+ guppy_basecaller -i <input path> -s <save path> --flowcell <flowcell name>\n+ --kit <kit name>\n+\n+List supported flowcells and kits::\n+\n+ guppy_basecaller --print_workflows\n+\n+Use server for basecalling::\n+\n+ guppy_basecaller -i <input path> -s <save path> -c <config file>\n+ --port <server address> [options]\n+\n+\n+**Command line parameters**::\n+\n+ --trim_threshold arg Threshold above which data will be trimmed\n+ (in standard deviations of current level\n+ distribution).\n+ --trim_min_events arg Adapter trimmer minimum stride intervals\n+ after stall that must be seen.\n+ --max_search_len arg Maximum number of samples to search through\n+ for the stall\n+ --override_scaling Manually provide scaling parameters rather\n+ than estimating them from each read.\n+ --scaling_med arg Median current value to use for manual\n+ scaling.\n+ --scaling_mad arg Median absolute deviation to use for manual\n+ scaling.\n+ --trim_strategy arg Trimming strategy to apply: \'dna\' or \'rna\'\n+ (or \'none\' to disable trimming)\n+ --dmean_win_size arg Window size for coarse stall event\n+ '..b' considered candidate calibration strands.\n+ --calib_min_coverage arg Minimum reference coverage to pass\n+ calibration strand detection.\n+ --print_workflows Output available workflows.\n+ --flowcell arg Flowcell to find a configuration for\n+ --kit arg Kit to find a configuration for\n+ -z [ --quiet ] Quiet mode. Nothing will be output to\n+ STDOUT if this option is set.\n+ --trace_categories_logs arg Enable trace logs - list of strings with\n+ the desired names.\n+ --verbose_logs Enable verbose logs.\n+ --disable_pings Disable the transmission of telemetry\n+ pings.\n+ --ping_url arg URL to send pings to\n+ --ping_segment_duration arg Duration in minutes of each ping segment.\n+ -q [ --records_per_fastq ] arg Maximum number of records per fastq file, 0\n+ means use a single file (per worker, per\n+ run id).\n+ --read_batch_size arg Maximum batch size, in reads, for grouping\n+ input files.\n+ --compress_fastq Compress fastq output files with gzip.\n+ -i [ --input_path ] arg Path to input fast5 files.\n+ --input_file_list arg Optional file containing list of input\n+ fast5 files to process from the input_path.\n+ -s [ --save_path ] arg Path to save fastq files.\n+ -l [ --read_id_list ] arg File containing list of read ids to filter\n+ to\n+ -r [ --recursive ] Search for input files recursively.\n+ --fast5_out Choice of whether to do fast5 output.\n+ --resume Resume a previous basecall run using the\n+ same output folder.\n+ --progress_stats_frequency arg Frequency in seconds in which to report\n+ progress statistics, if supplied will\n+ replace the default progress display.\n+ --max_block_size arg Maximum block size (in events) of basecall\n+ messages to server.\n+ -p [ --port ] arg Port for basecalling service.\n+ --barcoding_config_file arg Configuration file to use for barcoding.\n+ --num_barcode_threads arg Number of worker threads to use for\n+ barcoding.\n+ --disable_events Disable the transmission of event tables\n+ when receiving reads back from the basecall\n+ server.\n+ --client_id arg Optional unique identifier (non-negative\n+ integer) for this instance of the Guppy\n+ Client Basecaller, if supplied will form\n+ part of the output filenames.\n+ --nested_output_folder If flagged output fastq files will be\n+ written to a nested folder structure, based\n+ on: protocol_group/sample/protocol/qscore_p\n+ ass_fail/barcode_arrangement/\n+ -h [ --help ] produce help message\n+ -v [ --version ] print version number\n+ -c [ --config ] arg Config file to use\n+ -d [ --data_path ] arg Path to use for loading any data files the\n+ application requires.\n+\n+\n+------\n+ ]]></help>\n+</tool>\n' |