| Previous changeset 1:c1b6f5fbbcad (2019-02-01) Next changeset 3:56f1b7f06222 (2019-03-05) |
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Commit message:
Added config builder |
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modified:
galaxy/tools/concatenator/concatenator galaxy/tools/concatenator/concatenator.xml galaxy/tools/visualization/visualization.xml |
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added:
galaxy/tools/config_builder/config_builder galaxy/tools/config_builder/config_builder.xml |
| b |
| diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/concatenator/concatenator --- a/galaxy/tools/concatenator/concatenator Fri Feb 01 16:56:03 2019 -0500 +++ b/galaxy/tools/concatenator/concatenator Tue Mar 05 02:36:40 2019 -0500 |
| [ |
| @@ -6,9 +6,18 @@ parser = ap.ArgumentParser(prog='concatenater', conflict_handler='resolve', description="Concatenates all accessions and their associated paths") -input = parser.add_argument_group('Input', '') -input.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)") -input.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls") +subparser = parser.add_subparsers(dest='subcommand') + +variant_parser = subparser.add_parser(name='variant', help="Concatenate variant call files") +variant_parser.add_argument('-n', '--name', nargs='+', required=True, help="Sample name (accessions)") +variant_parser.add_argument('-i', '--input', nargs='+', required=True, help="Paths to calls") + +cluster_parser = subparser.add_parser('cluster') +cluster_parser.add_argument('--mlst', metavar="MLST", type=str, help="MLST clusters/distance matrix") +cluster_parser.add_argument('--snp', metavar="SNP", type=str, help="SNP clusters/distance matrix") +cluster_parser.add_argument('--cnv', metavar="CNV", type=str, help="CNV clusters/distance matrix") +cluster_parser.add_argument('--spoligo', metavar="SPOLIGO", type=str, help="Spoligotyping clusters/distance matrix") +# cluster_parser.add_argument('--kwip', metavar="KWIP", type=str, help="Kwip clusters/distance matrix") if len(sys.argv) == 1: parser.print_usage() @@ -17,5 +26,13 @@ args = parser.parse_args() output = open('paths.txt', 'w') -for index,path in enumerate(args.input): - output.write("%s=%s\n" % (args.name[index], path)) +if args.subcommand == 'variant': + for index,path in enumerate(args.input): + output.write("%s=%s\n" % (args.name[index], path)) +elif args.subcommand == 'cluster': + variant_types = [(args.mlst, 'MLST'), (args.snp, 'SNP'), (args.cnv, 'CNV'), (args.spoligo, 'spoligotyping')] + for variant in variant_types: + if variant[0] == None: + continue + else: + output.write("%s=%s\n" % (variant[1], variant[0])) |
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| diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/concatenator/concatenator.xml --- a/galaxy/tools/concatenator/concatenator.xml Fri Feb 01 16:56:03 2019 -0500 +++ b/galaxy/tools/concatenator/concatenator.xml Tue Mar 05 02:36:40 2019 -0500 |
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| @@ -5,12 +5,70 @@ </requirements> <command><![CDATA[ - $__tool_directory__/concatenator -n #for $path in $paths# ${path.element_identifier} #end for# - -i #for $path in $paths# $path #end for# + $__tool_directory__/concatenator + + #if $input_type.input_type_selector == "variant" + variant + -n #for $path in $input_type.paths# ${path.element_identifier} #end for# + -i #for $path in $input_type.paths# $path #end for# + #elif $input_type.input_type_selector == "clustering" + cluster + #if $input_type.mlst.mlst_checkbox + --mlst $input_type.mlst.mlst_path + #end if + #if $input_type.snp.snp_checkbox + --snp $input_type.snp.snp_path + #end if + #if $input_type.cnv.cnv_checkbox + --cnv $input_type.cnv.cnv_path + #end if + #if $input_type.spoligo.spoligo_checkbox + --spoligo $input_type.spoligo.spoligo_path + #end if + #end if ]]></command> + <inputs> - <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> + <conditional name="input_type"> + <param name="input_type_selector" type="select" label="Concatenation of variant calls, or clustering files"> + <option value="variant">Variant Call Files</option> + <option value="clustering">Clustering/Distance Matrix Files</option> + </param> + <when value="variant"> + <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> + </when> + <when value="clustering"> + <conditional name="mlst"> + <param name="mlst_checkbox" type="boolean" label="Include MLST"/> + <when value="true"> + <param name="mlst_path" type="data" label="MLST Clustering/Distance Matrix file" + format="txt,tabular"/> + </when> + </conditional> + <conditional name="snp"> + <param name="snp_checkbox" type="boolean" label="Include SNP"/> + <when value="true"> + <param name="snp_path" type="data" label="SNP Clustering/Distance Matrix file" + format="txt,tabular"/> + </when> + </conditional> + <conditional name="cnv"> + <param name="cnv_checkbox" type="boolean" label="Include CNV"/> + <when value="true"> + <param name="cnv_path" type="data" label="CNV Clustering/Distance Matrix file" + format="txt,tabular"/> + </when> + </conditional> + <conditional name="spoligo"> + <param name="spoligo_checkbox" type="boolean" label="Include Spoligotyping"/> + <when value="true"> + <param name="spoligo_path" type="data" label="Spoligotyping Clustering/Distance Matrix file" + format="txt,tabular"/> + </when> + </conditional> + </when> + </conditional> </inputs> <outputs> |
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| diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/config_builder/config_builder --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/config_builder/config_builder Tue Mar 05 02:36:40 2019 -0500 |
| [ |
| b'@@ -0,0 +1,185 @@\n+#!/usr/bin/env python\n+\n+import sys\n+import yaml\n+import argparse as ap\n+\n+parser = ap.ArgumentParser(prog=\'config_builder\', conflict_handler=\'resolve\',\n+ description="Builds the config file for PathOGiST")\n+\n+parser.add_argument(\'yaml\', help="Blank config file")\n+parser.add_argument(\'forward\', help="File to list of forward reads")\n+parser.add_argument(\'reverse\', help="File to list of reverse reads")\n+parser.add_argument(\'output\', help="Output prefix for final consensus clustering and visualization")\n+\n+tools = parser.add_argument_group(\'Tools\')\n+tools.add_argument(\'--snippy\', action=\'store_true\', help="Run Snippy")\n+tools.add_argument(\'--kwip\', action=\'store_true\', help="Run Kwip")\n+tools.add_argument(\'--prince\', action=\'store_true\', help="Run Prince")\n+tools.add_argument(\'--spotyping\', action=\'store_true\', help="Run Spotyping")\n+tools.add_argument(\'--mentalist\', action=\'store_true\', help="Run Mentalist")\n+\n+mentalist = parser.add_argument_group(\'Mentalist\')\n+mentalist.add_argument(\'--local_file\', action=\'store_true\', help="Use local database")\n+mentalist.add_argument(\'--build_db\', action=\'store_true\', help="Build a database")\n+mentalist.add_argument(\'--download_pubmlst\', action=\'store_true\', help="Download pubMLST scheme")\n+mentalist.add_argument(\'--download_cgmlst\', action=\'store_true\', help="Download cgMLST scheme")\n+mentalist.add_argument(\'--download_enterobase\', action=\'store_true\', help="Download Enterobase scheme")\n+\n+mentalist.add_argument(\'--local_db\', metavar="STRING", help="Location of database")\n+mentalist.add_argument(\'--kmer\', metavar="INT", help="Kmer size")\n+mentalist.add_argument(\'--fasta_files\', metavar="STRING", help="Location of FASTA files for MLST scheme")\n+mentalist.add_argument(\'--profile\', metavar="STRING", help="Profile file for known genotypes")\n+mentalist.add_argument(\'--scheme\', metavar="STRING", help="Species name or scheme ID")\n+mentalist.add_argument(\'--entero_scheme\', metavar="STRING", help="(S)almonella, (Y)ersinia, or (E)scherichia/Shigella")\n+mentalist.add_argument(\'--entero_type\', metavar="STRING", help="\'cg\' or \'wg\' for cgMLST or wgMLST, respectively.")\n+mentalist.add_argument(\'--mutation_threshold\', metavar="INT", help="Maximum number of mutations when looking for novel "\n+ "alleles")\n+mentalist.add_argument(\'--kt\', metavar="INT", help="Minimum number of times a kmer is seen to be considered present "\n+ "in the sample")\n+\n+kwip = parser.add_argument_group(\'Kwip\')\n+kwip.add_argument(\'--N\', metavar="INT", help="Number of tables")\n+kwip.add_argument(\'--x\', metavar="INT", help="Maximum table size")\n+kwip.add_argument(\'--ksize\', metavar="INT", help="kmer size to use")\n+kwip.add_argument(\'--unique_kmers\', metavar="INT", help="Approximate number of unique kmers in the input set")\n+\n+snippy = parser.add_argument_group(\'Snippy\')\n+snippy.add_argument(\'--reference\', metavar="STRING", help="Reference genome. Supports FASTA, GenBank, EMBL (not GFF)")\n+snippy.add_argument(\'--mapqual\', metavar="INT", help="Minimum read mapping quality to consider")\n+snippy.add_argument(\'--basequal\', metavar="INT", help="Minimum base quality to consider")\n+snippy.add_argument(\'--mincov\', metavar="INT", help="Minimum coverage of variant site")\n+snippy.add_argument(\'--minfrac\', metavar="FLOAT", help="Minimum proportion for variant evidence")\n+\n+clustering = parser.add_argument_group(\'Clustering\')\n+clustering.add_argument(\'--fine_snp\', action=\'store_true\', help="Use SNP as a fine datatype")\n+clustering.add_argument(\'--fine_mlst\', action=\'store_true\', help="Use MLST as a fine datatype")\n+clustering.add_argument(\'--fine_kwip\', action=\'store_true\', help="Use Kwip as a fine datatype")\n+clustering.add_argument(\'--fine_spoligo\', action=\'store_true\', help="Use Spoligotyping as a fine datatype")\n+clustering.add_argument(\'--fine_cnv\', action=\'store_true\', help="Use CNV as '..b'ard_reads\'] = args.forward\n+ list_doc[line][\'input_reads\'][\'reverse_reads\'] = args.reverse\n+\n+ if args.mentalist:\n+ if args.local_file:\n+ list_doc[line][\'mentalist\'][\'local_file\'][\'database\'] = args.local_db\n+ elif args.build_db:\n+ list_doc[line][\'mentalist\'][\'build_db\'][\'options\'][\'k\'] = args.kmer\n+ list_doc[line][\'mentalist\'][\'build_db\'][\'options\'][\'fasta_files\'] = args.fasta_files\n+ list_doc[line][\'mentalist\'][\'build_db\'][\'options\'][\'profile\'] = args.profile\n+ elif args.download_pubmlst:\n+ list_doc[line][\'mentalist\'][\'download_pubmlst\'][\'options\'][\'k\'] = args.kmer\n+ list_doc[line][\'mentalist\'][\'download_pubmlst\'][\'options\'][\'scheme\'] = args.scheme\n+ elif args.download_cgmlst:\n+ list_doc[line][\'mentalist\'][\'download_cgmlst\'][\'options\'][\'k\'] = args.kmer\n+ list_doc[line][\'mentalist\'][\'download_cgmlst\'][\'options\'][\'scheme\'] = args.scheme\n+ elif args.download_enterobase:\n+ list_doc[line][\'mentalist\'][\'download_enterobase\'][\'options\'][\'k\'] = args.kmer\n+ list_doc[line][\'mentalist\'][\'download_enterobase\'][\'options\'][\'scheme\'] = args.entero_scheme\n+ list_doc[line][\'mentalist\'][\'download_enterobase\'][\'options\'][\'type\'] = args.entero_type\n+\n+ if args.mutation_threshold:\n+ list_doc[line][\'mentalist\'][\'call\'][\'options\'][\'mutation_threshold\'] = args.mutation_threshold\n+ if args.kt:\n+ list_doc[line][\'mentalist\'][\'call\'][\'options\'][\'kt\'] = args.kt\n+\n+ if args.kwip:\n+ if args.N:\n+ list_doc[line][\'kwip\'][\'khmer_options\'][\'N\'] = args.N\n+ if args.x:\n+ list_doc[line][\'kwip\'][\'khmer_options\'][\'x\'] = args.x\n+ if args.ksize:\n+ list_doc[line][\'kwip\'][\'khmer_options\'][\'ksize\'] = args.ksize\n+ if args.unique_kmers:\n+ list_doc[line][\'kwip\'][\'khmer_options\'][\'unique-kmers\'] = args.unique_kmers\n+\n+ if args.snippy:\n+ list_doc[line][\'snippy\'][\'options\'][\'reference\'] = args.reference\n+ if args.mapqual:\n+ list_doc[line][\'snippy\'][\'options\'][\'mapqual\'] = args.mapqual\n+ if args.basequal:\n+ list_doc[line][\'snippy\'][\'options\'][\'basequal\'] = args.basequal\n+ if args.mincov:\n+ list_doc[line][\'snippy\'][\'options\'][\'mincov\'] = args.mincov\n+ if args.minfrac:\n+ list_doc[line][\'snippy\'][\'options\'][\'minfrac\'] = args.minfrac\n+\n+ if line == \'clustering\':\n+ list_doc[line][\'output_prefix\'] = args.output\n+\n+ fine = []\n+ if args.fine_snp:\n+ fine.append(\'SNP\')\n+ if args.fine_mlst:\n+ fine.append(\'MLST\')\n+ if args.fine_kwip:\n+ fine.append(\'kWIP\')\n+ if args.fine_spoligo:\n+ fine.append(\'spoligotyping\')\n+ if args.fine_cnv:\n+ fine.append(\'CNV\')\n+ list_doc[line][\'fine_clusterings\'] = fine\n+\n+ if args.snp_thresh:\n+ list_doc[line][\'thresholds\'][\'SNP\'] = args.snp_thresh\n+ if args.mlst_thresh:\n+ list_doc[line][\'thresholds\'][\'MLST\'] = args.snp_thresh\n+ if args.kwip_thresh:\n+ list_doc[line][\'thresholds\'][\'kWIP\'] = args.snp_thresh\n+ if args.spoligo_thresh:\n+ list_doc[line][\'thresholds\'][\'spoligotyping\'] = args.snp_thresh\n+ if args.cnv_thresh:\n+ list_doc[line][\'thresholds\'][\'CNV\'] = args.snp_thresh\n+\n+ if args.less_constraints:\n+ list_doc[line][\'all_constraints\'] = False\n+ if args.method:\n+ list_doc[line][\'method\'] = args.method\n+ if args.no_presolve:\n+ list_doc[line][\'presolve\'] = False\n+ if args.visualize:\n+ list_doc[line][\'visualize\'] = True\n+\n+with open("config.yaml", \'w\') as f:\n+ yaml.dump(list_doc, f)\n+\n' |
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| diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/config_builder/config_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy/tools/config_builder/config_builder.xml Tue Mar 05 02:36:40 2019 -0500 |
| [ |
| b'@@ -0,0 +1,243 @@\n+<tool id="config_builder" name="PathOGiST - Config Builder" version="1.0.0">\n+ <description>: Creates and populates the config file to run PathOGiST</description>\n+ <requirements>\n+ <requirement type="package" version="0.2.3">pathogist</requirement>\n+ </requirements>\n+\n+ <command><![CDATA[\n+ PATHOGIST all config.yaml --new_config\n+\n+ $__tool_directory__/config_builder\n+\n+ #if snippy.snippy_checkbox\n+ --snippy\n+ --reference $snippy.reference\n+ #if snippy.snippy_adv.snippy_adv_checkbox\n+ --mapqual $snippy.mapqual\n+ --basequal $snippy.basequal\n+ --mincov $snippy.mincov\n+ --minfrac $snippy.minfrac\n+ #endif\n+ $snippy.snp_fine\n+ --snp_thresh $snippy.snp_threshold\n+ #endif\n+\n+ #if mentalist.mentalist_checkbox\n+ --mentalist\n+ #if mentalist.db_loc.db_selector == "local_file"\n+ --local_file\n+ --local_db $mentalist.mlst_database\n+ #endif\n+ #if mentalist.db_loc.db_selector == "build_db"\n+ --build_db\n+ --kmer $mentalist.k\n+ --fasta_files $mentalist.fasta_files\n+ --profile $mentalist.profile\n+ #endif\n+ #if mentalist.db_loc.db_selector == "download_pubmlst"\n+ --download_pubmlst\n+ --kmer $mentalist.k\n+ --scheme $mentalist.scheme\n+ #endif\n+ #if mentalist.db_loc.db_selector == "download_cgmlst"\n+ --download_cgmlst\n+ --kmer $mentalist.k\n+ --scheme $mentalist.scheme\n+ #endif\n+ #if mentalist.db_loc.db_selector == "download_enterobase"\n+ --download_enterobase $mentalist.k\n+ --entero_scheme $mentalist.scheme\n+ --entero_type $mentalist.type\n+ #endif\n+ #if mentalist.mentalist_adv.mentalist_adv_checkbox\n+ --mutation_threshold $mentalist.mutation_thresh\n+ --kt $mentalist.kt\n+ #endif\n+ $mentalist.mlst_fine\n+ --mlst_thresh $mentalist.mlst_threshold\n+ #endif\n+\n+ #if prince.prince_checkbox\n+ --prince\n+ $prince.cnv_fine\n+ --cnv_thresh $prince.cnv_threshold\n+ #endif\n+\n+ #if kwip.kwip_checkbox\n+ --kwip\n+ #if kwip.kwip_adv.kwip_adv_checkbox\n+ --N $kwip.N\n+ --x $kwip.x\n+ --ksize $kwip.ksize\n+ --unique_kmers $kwip.unique_kmers\n+ #endif\n+ $kwip.kwip_fine\n+ --kwip_thresh $kwip.kwip_threshold\n+ #endif\n+\n+ #if spotyping.spotyping_checkbox\n+ --spotyping\n+ $spotyping.spoligo_fine\n+ --spoligo_thresh $spotyping.spoligo_threshold\n+ #endif\n+\n+ #if adv_clustering.adv_clustering_checkbox\n+ $adv_clustering.all_constraints\n+ --method $adv_clustering.method\n+ $adv_clustering.presolve\n+ $adv_clustering.visualize\n+ #endif\n+ ]]></command>\n+\n+\n+ <inputs>\n+ <!--<conditional name="task">-->\n+ <!--<param name="task_selector" type="select" label="Create Blank Config or Populate Config File">-->\n+ <!--<option value="create">Create Blank Config File</option>-->\n+ <!--<option value="populate">Populate Config File</option>-->\n+ <!--</param>-->\n+ <!--<when value="create">-->\n+\n+ <!--</when>-->\n+ <!--<when value="populate">-->\n+ <conditional name="snippy">\n+ <param name="snippy_checkbox" type="boolean" label="Run Snippy"/>\n+ <when value="true">\n+ <param name="reference" type="data" format="fasta,fa,fasta.gz,fa.gz" label="Reference Genome"/>\n+ <con'..b'"Maximum number of\n+ mutations when looking for novel alleles"/>\n+ <param name="kt" type="integer" value="10" min="1" label="Minimum number of times a\n+ kmer is seen to be considered present in the sample"/>\n+ </when>\n+ </conditional>\n+ <param name="mlst_fine" type="boolean" label="Consider MLST as a fine datatype"/>\n+ <param name="mlst_threshold" type="integer" value="300" min="0"\n+ label="Correlation clustering threshold for MLST"/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="prince">\n+ <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>\n+ <when value="true">\n+ <param name="cnv_fine" type="boolean" label="Consider CNV as a fine datatype"/>\n+ <param name="cnv_threshold" type="integer" value="100" min="0"\n+ label="Correlation clustering threshold for CNV"/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="kwip">\n+ <param name="kwip_checkbox" type="boolean" label="Run kWIP"/>\n+ <when value="true">\n+ <conditional name="kwip_adv">\n+ <param name="kwip_adv_checkbox" type="boolean" label="Advance kWIP Parameters"/>\n+ <when value="true">\n+ <param name="N" type="integer" value="1" min="1" label="Number of tables"/>\n+ <param name="x" type="float" value="1e9" min="1" label="Maximum table size"/>\n+ <param name="ksize" type="integer" value="31" min="1" label="kmer size"/>\n+ <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number\n+ of unique kmers in the input set"/>\n+ </when>\n+ </conditional>\n+ <param name="kwip_fine" type="boolean" label="Consider kWIP as a fine datatype"/>\n+ <param name="kwip_threshold" type="float" value="0.4" min="0"\n+ label="Correlation clustering threshold for kWIP"/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="spotyping">\n+ <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>\n+ <when value="true">\n+ <param name="spoligo_fine" type="boolean" label="Consider spoligotype as a fine datatype"/>\n+ <param name="spoligo_threshold" type="integer" value="8" min="0"\n+ label="Correlation clustering threshold for Spoligotyping"/>\n+ </when>\n+ </conditional>\n+\n+ <conditional name="adv_clustering">\n+ <param name="adv_clustering_checkbox" type="boolean"\n+ label="Advanced settings for correlation and consensus clustering"/>\n+ <when value="true">\n+ <param name="all_constraints" type="boolean" checked="true" falsevalue="--less_constraints"\n+ truevalue="" label="Use all constraints when performing clustering"/>\n+ <param name="method" type="text" value="C4" size="3"\n+ label="`C4` or `ILP` method for clustering algorithm"/>\n+ <param name="presolve" type="boolean" checked="true" falsevalue="--no_presolve" truevalue=""\n+ label="Perform presolving for clustering"/>\n+ <param name="visualize" type="boolean" checked="false" falsevalue="" truevalue="--visualize"\n+ label="Visualize clusters"/>\n+ </when>\n+ </conditional>\n+ <!--</when>-->\n+ <!--</conditional>-->\n+ </inputs>\n+\n+ <outputs>\n+ <data name="output" label="PathOGiST Config File" format="yaml" from_work_dir="config.yaml"/>\n+ </outputs>\n+\n+ <help>\n+\n+ </help>\n+\n+ <citations>\n+\n+ </citations>\n+</tool>\n' |
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| diff -r c1b6f5fbbcad -r baf1e89b42eb galaxy/tools/visualization/visualization.xml --- a/galaxy/tools/visualization/visualization.xml Fri Feb 01 16:56:03 2019 -0500 +++ b/galaxy/tools/visualization/visualization.xml Tue Mar 05 02:36:40 2019 -0500 |
| [ |
| @@ -5,7 +5,7 @@ </requirements> <command><![CDATA[ - PATHOGIST vis $distance $sample $pdf + PATHOGIST visualize $distance $sample $pdf ]]></command> <inputs> |