def get_contract_parser(): """Get tool contract parser. Input: idx 0 - HQ isoforms fastq as gmap input idx 1 - gmap reference set Output: idx 0 - gmap output SAM """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_map_isoforms_io_arguments(p.arg_parser.parser) add_gmap_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.FASTQ, "hq_isoforms_fastq", "FASTQ In", "HQ isoforms FASTQ file") # input 0 tcp.add_input_file_type(FileTypes.DS_GMAP_REF, "gmap_referenceset", "GmapReferenceSet In", "Gmap reference set file") # input 1 tcp.add_output_file_type(FileTypes.SAM, "gmap_output_sam", name="SAM file", description="Gmap output sam", default_name="gmap_output") tcp.add_int(option_id=Constants.GMAP_NPROC_ID, option_str="gmap_nproc", default=Constants.GMAP_NPROC_DEFAULT, name="GMAP nproc", description="GMAP nproc") return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - HQ isoforms fastq as gmap input idx 1 - gmap reference set Output: idx 0 - gmap output SAM """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_map_isoforms_io_arguments(p.arg_parser.parser) add_gmap_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.FASTQ, "hq_isoforms_fastq", "FASTQ In", "HQ isoforms FASTQ file") # input 0 tcp.add_input_file_type(FileTypes.DS_GMAP_REF, "gmap_referenceset", "GmapReferenceSet In", "Gmap reference set file") # input 1 tcp.add_output_file_type(FileTypes.SAM, "gmap_output_sam", name="Gmap SAM Mapping HQ Isoforms to Genome", description="Gmap output sam mapping HQ isoforms to reference", default_name="gmap_output") tcp.add_int(option_id=Constants.GMAP_NPROC_ID, option_str="gmap_nproc", default=Constants.GMAP_NPROC_DEFAULT, name="GMAP nproc", description="GMAP nproc") return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - group file idx 1 - pickle file Output: idx 0 - read stat file idx 1 - abundance file """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_make_abundance_io_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type( FileTypes.TXT, "group_txt", "TXT In", "Group file associating isoforms with reads") # input 0 tcp.add_input_file_type( FileTypes.PICKLE, "hq_lq_pre_dict", "PICKLE In", "Pickle file containing dicts mapping HQ (LQ) " + "sample prefixes to ICE cluster output directories") # input 1 tcp.add_output_file_type(FileTypes.TXT, "read_stat_txt", name="TXT file", description="Read status of FL and nFL reads", default_name="output_mapped_read_stat") tcp.add_output_file_type(FileTypes.TXT, "abundance_txt", name="TXT file", description="Abundance file", default_name="output_mapped_abundance") return p
def get_contract_parser(): p = get_base_contract_parser(Constants, default_level="DEBUG") tcp = p.tool_contract_parser add_fofn_arguments(p.arg_parser.parser, bas_fofn=True, tool_contract_parser=tcp) tcp.add_input_file_type(FileTypes.DS_CONTIG, "consensus_fa", name="Consensus isoforms", description="ContigSet of consensus isoforms") tcp.add_input_file_type(FileTypes.PICKLE, "cluster_pickle", name="Clusters", description="Cluster pickle file") tcp.add_input_file_type( FileTypes.PICKLE, "map_nofl_pickle", name="Pickle file", description="Pickle file for non-full-length read mapping") tcp.add_input_file_type(FileTypes.JSON, "json_in", name="JSON file", description="Sentinel file from ice_quiver task") add_cluster_summary_report_arguments(p) add_ice_post_quiver_hq_lq_arguments(p) return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - group file idx 1 - pickle file Output: idx 0 - read stat file idx 1 - abundance file """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_make_abundance_io_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.TXT, "group_txt", "TXT In", "Group file associating isoforms with reads") # input 0 tcp.add_input_file_type(FileTypes.PICKLE, "hq_lq_pre_dict", "PICKLE In", "Pickle file containing dicts mapping HQ (LQ) " + "sample prefixes to ICE cluster output directories") # input 1 tcp.add_output_file_type(FileTypes.TXT, "read_stat_txt", name="TXT file", description="Read status of FL and nFL reads", default_name="output_mapped_read_stat") tcp.add_output_file_type(FileTypes.TXT, "abundance_txt", name="TXT file", description="Abundance file", default_name="output_mapped_abundance") return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - A FASTQ file containing uncollapsed isoforms (hq_polished) idx 1 - A SORTED GMAP SAM file containing alignments mapping uncollapsed isoforms to reference genomes (produced by map_isoforms_to_genome) idx 2 - A Pickle file containing dicts mapping HQ (LQ) sample prefixes to ICE cluster output directories(e.g., hq_lq_pre_dict.pickle) Output: idx 0 - A FASTQ file containing representative sequences of filtered collapsed isoforms idx 1 - A GFF file containing collapsed filtered isoforms idx 2 - A Abundnace file containing abundance info of collapsed filtered isoforms idx 3 - A Group file which associates collapsed isoforms with uncollapsed isoforms idx 4 - A ReadStat file containing FL and nFL read status """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_post_mapping_to_genome_io_arguments(p.arg_parser.parser) add_post_mapping_to_genome_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.FASTQ, "hq_isoforms_fq", "FASTQ In", "Input HQ polished isoforms in FASTQ file") # input 0 tcp.add_input_file_type(FileTypes.SAM, "sorted_gmap_sam", "SAM In", "Sorted GMAP SAM file") # input 1 tcp.add_input_file_type(FileTypes.PICKLE, "hq_lq_pre_dict", "PICKLE In", "Pickle file containing dicts mapping HQ (LQ) " + "sample prefixes to ICE cluster output directories") # input 2 tcp.add_output_file_type(FileTypes.FASTQ, "collapsed_filtered_isoforms_fq", name="FASTQ file", description="Representative sequences of collapsed filtered isoforms", default_name="output_mapped") # output 0 tcp.add_output_file_type(FileTypes.GFF, "collapsed_filtered_isoforms_gff", name="GFF file", description="Collapsed filtered isoforms gff", default_name="output_mapped") # output 1 tcp.add_output_file_type(FileTypes.TXT, "abundance_txt", name="TXT file", description="Abundance file", default_name="output_mapped_abundance") # output 2 tcp.add_output_file_type(FileTypes.TXT, "groups_txt", name="TXT file", description="Collapsed isoform groups", default_name="output_mapped_groups") # output 3 tcp.add_output_file_type(FileTypes.TXT, "read_stat_txt", name="TXT file", description="Read status of FL and nFL reads", default_name="output_mapped_read_stat") # output 3 # Add tcp options add_post_mapping_to_genome_tcp_options(tcp) return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - group txt file idx 1 - abundance txt file idx 2 - gff file idx 3 - rep fastq file Output: idx 0 - abundance file idx 1 - gff file idx 2 - rep fastq file """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_filter_collapsed_isoforms_io_arguments(p.arg_parser.parser) add_filter_collapsed_isoforms_arguments(p.arg_parser.parser) # DONT move --max_fuzzy_junction to add_filter_collapsed_isoforms_arguments p.arg_parser.parser.add_argument( "--max_fuzzy_junction", type=int, default=ci.Constants.MAX_FUZZY_JUNCTION_DEFAULT, help=ci.Constants.MAX_FUZZY_JUNCTION_DESC) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type( FileTypes.TXT, "group_txt", "TXT In", "Group file associating isoforms with reads") # input 0 tcp.add_input_file_type(FileTypes.TXT, "abundance_txt", "TXT In", "Abundance file") # input 1 tcp.add_input_file_type(FileTypes.GFF, "collapsed_isoforms_gff", "GFF In", "GFF file") # input 2 tcp.add_input_file_type( FileTypes.FASTQ, "rep_fastq", "FASTQ In", "Representative sequences of collapsed isoforms in FATSQ") # input 3 tcp.add_output_file_type( FileTypes.TXT, "abundance_txt", name="TXT file", description="Abundance file", default_name="output_mapped_filtered_abundance") # output 0 tcp.add_output_file_type(FileTypes.GFF, "collapsed_isoforms_gff", name="GFF file", description="Collapsed isoforms in GFF file", default_name="output_mapped_filtered") # output 1 tcp.add_output_file_type( FileTypes.FASTQ, "rep_fastq", name="FASTQ file", description="Representative sequences of collapsed isoforms in FASTQ", default_name="output_mapped_filtered") # output 2 add_filter_collapsed_isoforms_tcp_options(tcp) return p
def get_contract_parser(): """ Return resolved tool contract. input files: idx 0 - ChunkTasksPickle of ClusterChunkTask objects idx 1 - sentinel txt output files: idx 0 - consensus_isoforms.fa idx 1 - summary.json idx 2 - cluster_report.csv idx 3 - hq_isoforms.contigset.xml idx 4 - hq_isoforms.fq idx 5 - lq_isoforms.contigset.xml idx 6 - lq_isoforms.fq idx 7 - hq_lq_prefix_dict.pickle """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In", "Cluster chunks pickle file") # input 0 p.add_input_file_type(FileTypes.TXT, "cluster_sentinel_in", "Sentinel In", "Setinel file") # input idx 1 # output idx 0, consensus_isoforms.contigset, p.add_output_file_type(FileTypes.DS_CONTIG, "consensus_isoforms", name="Unpolished Consensus Isoforms", description="Output unpolished consensus isoforms", default_name="consensus_isoforms") # output idx 1, summary.json, # output idx 2, cluster_report.csv add_cluster_summary_report_arguments(p) # output idx 3, hq_isoforms_fa, idx 4, hq_isoforms_fq, # idx 5 lq_isoforms_fa, idx 6 lq_isoforms_fq add_ice_post_quiver_hq_lq_arguments(p) # output idx 7, hq_lq_prefix_dict.pickle p.add_output_file_type( FileTypes.PICKLE, "hq_lq_prefix_dict", name="HQ LQ Sample Prefix Dict", description="Pickle mapping HQ (LQ) sample prefixes to ICE dir", default_name="hq_lq_prefix_dict") # user specified sample name. p.add_str(option_id=Constants.SAMPLE_NAME_ID, option_str="sample_name", default=Constants.SAMPLE_NAME_DEFAULT, name="sample Name", description="Sample Name") return p
def get_contract_parser(): """ Return resolved tool contract. input files: idx 0 - ChunkTasksPickle of ClusterChunkTask objects idx 1 - sentinel txt output files: idx 0 - consensus_isoforms.fa idx 1 - summary.json idx 2 - cluster_report.csv idx 3 - hq_isoforms.contigset.xml idx 4 - hq_isoforms.fq idx 5 - lq_isoforms.contigset.xml idx 6 - lq_isoforms.fq idx 7 - hq_lq_prefix_dict.pickle """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In", "Cluster chunks pickle file") # input 0 p.add_input_file_type(FileTypes.TXT, "cluster_sentinel_in", "Sentinel In", "Setinel file") # input idx 1 # output idx 0, consensus_isoforms.contigset, p.add_output_file_type(FileTypes.DS_CONTIG, "consensus_isoforms", name="Unpolished Consensus Isoforms", description="Output unpolished consensus isoforms", default_name="consensus_isoforms") # output idx 1, summary.json, # output idx 2, cluster_report.csv add_cluster_summary_report_arguments(p) # output idx 3, hq_isoforms_fa, idx 4, hq_isoforms_fq, # idx 5 lq_isoforms_fa, idx 6 lq_isoforms_fq add_ice_post_quiver_hq_lq_arguments(p) # output idx 7, hq_lq_prefix_dict.pickle p.add_output_file_type(FileTypes.PICKLE, "hq_lq_prefix_dict", name="HQ LQ Sample Prefix Dict", description="Pickle mapping HQ (LQ) sample prefixes to ICE dir", default_name="hq_lq_prefix_dict") # user specified sample name. p.add_str(option_id=Constants.SAMPLE_NAME_ID, option_str="sample_name", default=Constants.SAMPLE_NAME_DEFAULT, name="sample Name", description="Sample Name") return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - group txt file idx 1 - abundance txt file idx 2 - gff file idx 3 - rep fastq file Output: idx 0 - abundance file idx 1 - gff file idx 2 - rep fastq file """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_filter_collapsed_isoforms_io_arguments(p.arg_parser.parser) add_filter_collapsed_isoforms_arguments(p.arg_parser.parser) # DONT move --max_fuzzy_junction to add_filter_collapsed_isoforms_arguments p.arg_parser.parser.add_argument("--max_fuzzy_junction", type=int, default=ci.Constants.MAX_FUZZY_JUNCTION_DEFAULT, help=ci.Constants.MAX_FUZZY_JUNCTION_DESC) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.TXT, "group_txt", "TXT In", "Group file associating isoforms with reads") # input 0 tcp.add_input_file_type(FileTypes.TXT, "abundance_txt", "TXT In", "Abundance file") # input 1 tcp.add_input_file_type(FileTypes.GFF, "collapsed_isoforms_gff", "GFF In", "GFF file") # input 2 tcp.add_input_file_type(FileTypes.FASTQ, "rep_fastq", "FASTQ In", "Representative sequences of collapsed isoforms in FATSQ") # input 3 tcp.add_output_file_type(FileTypes.TXT, "abundance_txt", name="TXT file", description="Abundance file", default_name="output_mapped_filtered_abundance") # output 0 tcp.add_output_file_type(FileTypes.GFF, "collapsed_isoforms_gff", name="GFF file", description="Collapsed isoforms in GFF file", default_name="output_mapped_filtered") # output 1 tcp.add_output_file_type(FileTypes.FASTQ, "rep_fastq", name="FASTQ file", description="Representative sequences of collapsed isoforms in FASTQ", default_name="output_mapped_filtered") # output 2 add_filter_collapsed_isoforms_tcp_options(tcp) return p
def get_contract_parser(): p = get_base_contract_parser(Constants, default_level="DEBUG") arg_parser = p.arg_parser.parser tcp = p.tool_contract_parser add_fofn_arguments(arg_parser, bas_fofn=True, tool_contract_parser=tcp) tcp.add_input_file_type(FileTypes.DS_CONTIG, "consensus_fa", name="ContigSet", description="Consensus isoforms") tcp.add_input_file_type(FileTypes.PICKLE, "cluster_pickle", name="Clusters", description="Cluster pickle file") tcp.add_input_file_type(FileTypes.PICKLE, "map_nofl_pickle", name="Pickle file", description="Pickle file for non-full-length read mapping") # XXX this file does nothing other than connect this task to # ice_quiver_postprocess in pbsmrtpipe tcp.add_output_file_type(FileTypes.JSON, "json_out", "JSON file", "JSON sentinel file", default_name="quiver_out") return p
def get_contract_parser(): p = get_base_contract_parser(Constants, default_level="DEBUG") tcp = p.tool_contract_parser add_fofn_arguments(p.arg_parser.parser, bas_fofn=True, tool_contract_parser=tcp) tcp.add_input_file_type(FileTypes.DS_CONTIG, "consensus_fa", name="Consensus isoforms", description="ContigSet of consensus isoforms") tcp.add_input_file_type(FileTypes.PICKLE, "cluster_pickle", name="Clusters", description="Cluster pickle file") tcp.add_input_file_type(FileTypes.PICKLE, "map_nofl_pickle", name="Pickle file", description="Pickle file for non-full-length read mapping") tcp.add_input_file_type(FileTypes.JSON, "json_in", name="JSON file", description="Sentinel file from ice_quiver task") add_cluster_summary_report_arguments(p) add_ice_post_quiver_hq_lq_arguments(p) return p
def get_contract_parser(): """ Return resolved tool contract. input files: idx 0 - ChunkTasksPickle of ClusterChunkTask objects idx 1 - ice_polish_cluster_bins sentinel txt output files: idx 0 - sentinal """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In", "Cluster chunks pickle file") # input idx 0 p.add_input_file_type(FileTypes.TXT, "ice_polish_cluster_bins_sentinel", "Sentinel In", "Setinel file") # input idx 1 # output idx 0, consensus_isoforms.contigset, p.add_output_file_type(FileTypes.TXT, "ice_cleanup_sentinel", name="Sentinel file", description="Output sentinel file", default_name="ice_cleanup_done") return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - Output: idx 0 - reads which can represent collapsed isoforms in CONTIGSET idx 1 - collapsed isoforms in GFF idx 2 - collapsed isoform groups in TXT """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_collapse_mapped_isoforms_io_arguments(p.arg_parser.parser) add_collapse_mapped_isoforms_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type( FileTypes.DS_CONTIG, "hq_isoforms_ds", "ContigSet In", "Input HQ polished isoforms in ContigSet file") # input 0 tcp.add_input_file_type(FileTypes.SAM, "sorted_gmap_sam", "SAM In", "Sorted GMAP SAM file") # input 1 tcp.add_output_file_type( FileTypes.DS_CONTIG, "collapsed_isoforms_rep_ds", name="Collapsed isoforms", description="Representative reads of collapsed isoforms", default_name="output") # output 0 tcp.add_output_file_type(FileTypes.GFF, "collapsed_isoforms_gff", name="Collapsed isoforms GFF", description="Collapsed isoforms gff", default_name="output") # output 1 tcp.add_output_file_type(FileTypes.TXT, "groups_txt", name="TXT file", description="Collapsed isoform groups", default_name="output_groups") # output 2 add_collapse_mapped_isoforms_tcp_options(tcp) return p
def get_contract_parser(): """ Return tool contract parser for running ICE clustering no quiver, no sge setting needed. The tool contract parser has 2 inputs: idx 0 - cluster_chunks.pickle (original or spawned) idx 1 - ccs, and has one outputs: idx 0 - cluster_chunk_done.txt, a sential file which does nothing but connect ICE cluster and the subsequence ice_partial """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In", "Cluster chunks pickle file") # input 0 p.add_input_file_type(FileTypes.DS_CCS, "ccs_in", "ConsensusReadSet In", "PacBio ConsensusReadSet") # input 1 p.add_output_file_type(FileTypes.TXT, "cluster done txt", name="Cluster Done Txt file", description="Cluster Done Txt file.", default_name="cluster_chunks_done") return p
def get_contract_parser(): """ input idx 0: polish_chunk_pickle_id input idx 1: sentinel.txt input idx 2: *.subreadset.xml output idx 0: chunk json """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "polish_chunk_pickle", "PICKLE", "Polish Chunk Tasks Pickle") # input idx 0 p.add_input_file_type(FileTypes.TXT, "sentinel_in", "Sentinel In", "Setinel file") # input idx 1 p.add_input_file_type(FileTypes.DS_SUBREADS, "subreads_in", "SubreadSet In", "PacBio SubreadSet") # input idx 2 # this file does nothing other than connect pbsmrtpipe tasks p.add_output_file_type(FileTypes.TXT, "polish done txt", name="Polish Done Txt file", description="Polish Done Txt file.", default_name="polish_chunks_done") return p
def get_contract_parser(): p = get_base_contract_parser(Constants, default_level="DEBUG") add_cluster_arguments(p) p.tool_contract_parser.add_output_file_type( FileTypes.PICKLE, "pickle_fn", name="Clusters pickle file", description="Python pickle file of clusters", default_name="final_clusters") # rtc has 4 inputs: # idx 0 - flnc.contigset, # idx 1 - nfl.contigset, # idx 2 - ccs, # idx 3 - subreads # # rtc has 4 outputs: # idx 0 - consensus_isoform.contigset, # idx 1 - output.json, # idx 2 - output.csv # idx 3 - output.pickle return p
def get_contract_parser(): """Return a tool contract parser for separate_flnc. Input: idx 0 - flnc.fa|fq|ds Output: idx 0 - out.pickle """ p = get_base_contract_parser(Constants, default_level="DEBUG") add_separate_flnc_io_arguments(p.arg_parser.parser) add_separate_flnc_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.DS_CONTIG, "flnc_fa", name="FASTA or ContigSet file", description="FLNC reads ContigSet") tcp.add_output_file_type(FileTypes.PICKLE, "out_pickle", default_name="separate_flnc", name="Bins of FLNC Reads", description="output bins in pickle.") add_separate_flnc_tcp_options(tcp) return p
def get_contract_parser(): """Tool contract should have the following inputs and outputs. input: idx 0: partial_chunks.pickle idx 1: ccs idx 2: sentinel txt file output idx 0 - partial_chunk_done.txt, a sential file which does nothing but connect ice_partial and the subsequence task combine_ice_partial """ p = get_base_contract_parser(Constants, default_level="DEBUG") p.add_input_file_type(FileTypes.PICKLE, "partial_chunks_pickle", "Pickle In", "Partial chunks pickle file") # input 0 p.add_input_file_type(FileTypes.TXT, "partial_sentinel_in", "Sentinel In", "Setinel file") # input 1 p.add_input_file_type(FileTypes.DS_CCS, "ccs_in", "ConsensusReadSet In", "PacBio ConsensusReadSet") # input 2 p.add_output_file_type(FileTypes.TXT, "partial done txt", name="Partial Done Txt file", description="Partial Done Txt file.", default_name="partial_chunks_done") return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - Output: idx 0 - reads which can represent collapsed isoforms in CONTIGSET idx 1 - collapsed isoforms in GFF idx 2 - collapsed isoform groups in TXT """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_collapse_mapped_isoforms_io_arguments(p.arg_parser.parser) add_collapse_mapped_isoforms_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.DS_CONTIG, "hq_isoforms_ds", "ContigSet In", "Input HQ polished isoforms in ContigSet file") # input 0 tcp.add_input_file_type(FileTypes.SAM, "sorted_gmap_sam", "SAM In", "Sorted GMAP SAM file") # input 1 tcp.add_output_file_type(FileTypes.DS_CONTIG, "collapsed_isoforms_rep_ds", name="Collapsed isoforms", description="Representative reads of collapsed isoforms", default_name="output") # output 0 tcp.add_output_file_type(FileTypes.GFF, "collapsed_isoforms_gff", name="Collapsed isoforms GFF", description="Collapsed isoforms gff", default_name="output") # output 1 tcp.add_output_file_type(FileTypes.TXT, "groups_txt", name="TXT file", description="Collapsed isoform groups", default_name="output_groups") # output 2 add_collapse_mapped_isoforms_tcp_options(tcp) return p
def get_contract_parser(): """Return a tool contract parser for separate_flnc. Input: idx 0 - flnc.fa|fq|ds Output: idx 0 - out.pickle """ p = get_base_contract_parser(Constants, default_level="DEBUG") add_separate_flnc_io_arguments(p.arg_parser.parser) add_separate_flnc_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type(FileTypes.DS_CONTIG, "flnc_fa", name="FASTA or ContigSet file", description="FLNC reads ContigSet") tcp.add_output_file_type(FileTypes.PICKLE, "out_pickle", default_name="separate_flnc", name="Binned transcripts pickle file", description="output bins in pickle.") add_separate_flnc_tcp_options(tcp) return p
def get_contract_parser(): p = get_base_contract_parser(Constants, default_level="INFO") add_ice_partial_one_arguments(p) return p
def get_contract_parser(): p = get_base_contract_parser(Constants) add_subset_arguments(p) return p
def get_contract_parser(): """Get tool contract parser. Input: idx 0 - A FASTQ file containing uncollapsed isoforms (hq_polished) idx 1 - A SORTED GMAP SAM file containing alignments mapping uncollapsed isoforms to reference genomes (produced by map_isoforms_to_genome) idx 2 - A Pickle file containing dicts mapping HQ (LQ) sample prefixes to ICE cluster output directories(e.g., hq_lq_pre_dict.pickle) Output: idx 0 - A FASTQ file containing representative sequences of filtered collapsed isoforms idx 1 - A GFF file containing collapsed filtered isoforms idx 2 - A Abundnace file containing abundance info of collapsed filtered isoforms idx 3 - A Group file which associates collapsed isoforms with uncollapsed isoforms idx 4 - A ReadStat file containing FL and nFL read status """ p = get_base_contract_parser(Constants, default_level="DEBUG") # argument parser add_post_mapping_to_genome_io_arguments(p.arg_parser.parser) add_post_mapping_to_genome_arguments(p.arg_parser.parser) # tool contract parser tcp = p.tool_contract_parser tcp.add_input_file_type( FileTypes.FASTQ, "hq_isoforms_fq", "FASTQ In", "Input HQ polished isoforms in FASTQ file") # input 0 tcp.add_input_file_type(FileTypes.SAM, "sorted_gmap_sam", "SAM In", "Sorted GMAP SAM file") # input 1 tcp.add_input_file_type( FileTypes.PICKLE, "hq_lq_pre_dict", "PICKLE In", "Pickle file containing dicts mapping HQ (LQ) " + "sample prefixes to ICE cluster output directories") # input 2 tcp.add_output_file_type( FileTypes.FASTQ, "collapsed_filtered_isoforms_fq", name="Collapsed Filtered Isoforms", description="Representative sequences of collapsed filtered isoforms", default_name="output_mapped") # output 0 tcp.add_output_file_type(FileTypes.GFF, "collapsed_filtered_isoforms_gff", name="Collapsed Filtered Isoforms", description="Collapsed filtered isoforms gff", default_name="output_mapped") # output 1 tcp.add_output_file_type( FileTypes.TXT, "abundance_txt", name="Isoform Abundance", description="Abundance file", default_name="output_mapped_abundance") # output 2 tcp.add_output_file_type(FileTypes.TXT, "groups_txt", name="Collapsed Isoform Groups", description="Collapsed isoform groups", default_name="output_mapped_groups") # output 3 tcp.add_output_file_type( FileTypes.TXT, "read_stat_txt", name="FL nFL Reads Status", description="Read status of FL and nFL reads", default_name="output_mapped_read_stat") # output 4 # Add tcp options add_post_mapping_to_genome_tcp_options(tcp) return p
def get_contract_parser(): """Get PbParser for classify.""" p = get_base_contract_parser(Constants, default_level="DEBUG") add_classify_arguments(p) return p