| Previous changeset 8:7708da43aefb (2019-03-11) |
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Commit message:
New Concatenator |
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modified:
galaxy/tools/concatenator/concatenator galaxy/tools/concatenator/concatenator.xml |
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| diff -r 7708da43aefb -r 728c6b81b45e galaxy/tools/concatenator/concatenator --- a/galaxy/tools/concatenator/concatenator Mon Mar 11 03:27:37 2019 -0400 +++ b/galaxy/tools/concatenator/concatenator Mon Mar 11 12:46:41 2019 -0400 |
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| @@ -17,22 +17,37 @@ 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") +cluster_parser.add_argument('--kwip', metavar="KWIP", type=str, help="Kwip clusters/distance matrix") + +reads_parser = subparser.add_parser('reads') +reads_parser.add_argument('forward', help="Forward reads") +reads_parser.add_argument('reverse', help="Reverse reads") if len(sys.argv) == 1: parser.print_usage() sys.exit(1) args = parser.parse_args() -output = open('paths.txt', 'w') if args.subcommand == 'variant': + output = open('paths.txt', 'w') for index,path in enumerate(args.input): output.write("%s=%s\n" % (args.name[index], path)) + output.close() + elif args.subcommand == 'cluster': - variant_types = [(args.mlst, 'MLST'), (args.snp, 'SNP'), (args.cnv, 'CNV'), (args.spoligo, 'spoligotyping')] + output = open('paths.txt', 'w') + variant_types = [(args.mlst, 'MLST'), (args.snp, 'SNP'), (args.cnv, 'CNV'), (args.spoligo, 'spoligotyping'), + (args.kwip, 'kWIP')] for variant in variant_types: if variant[0] == None: continue else: output.write("%s=%s\n" % (variant[1], variant[0])) + output.close() + +elif args.subcommand == 'reads': + with open('forward.txt', 'a') as f_out: + f_out.write(args.forward) + with open('reverse.txt', 'a') as r_out: + r_out.write(args.reverse) |
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| diff -r 7708da43aefb -r 728c6b81b45e galaxy/tools/concatenator/concatenator.xml --- a/galaxy/tools/concatenator/concatenator.xml Mon Mar 11 03:27:37 2019 -0400 +++ b/galaxy/tools/concatenator/concatenator.xml Mon Mar 11 12:46:41 2019 -0400 |
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| @@ -25,6 +25,10 @@ #if $input_type.spoligo.spoligo_checkbox --spoligo $input_type.spoligo.spoligo_path #end if + #elif $input_type.input_type_selector == "reads" + reads + $input_type.fastq.forward + $input_type.fastq.reverse #end if ]]></command> @@ -34,6 +38,7 @@ <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> + <option value="reads">Raw reads</option> </param> <when value="variant"> <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> @@ -68,11 +73,24 @@ </when> </conditional> </when> + <when value="reads"> + <param name="fastq" type="data_collection" collection_type="paired" + format="fastqsanger,fastq,fastq.gz,fastqsanger.gz" label="Select paired collection"/> + </when> </conditional> </inputs> <outputs> - <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/> + <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"> + <filter>input_type[input_type_selector] == 'variant' + or input_type[input_type_selector] == 'clustering'</filter> + </data> + <data name="forward" label="Paths of ${on_string} (forward reads)" format="txt" from_work_dir="forward.txt"> + <filter>input_type[input_type_selector] == 'reads'</filter> + </data> + <data name="reverse" label="Paths of ${on_string} (reverse reads)" format="txt" from_work_dir="reverse.txt"> + <filter>input_type[input_type_selector] == 'reads'</filter> + </data> </outputs> <help> |