Loading debian/README.sourcedeleted 100644 → 0 +0 −4 Original line number Diff line number Diff line The cwl/ directory was generated thusly: All binaries were called with --write-ctd and those CTDs were converted to CWL using https://github.com/WorkflowConversion/CTDConverter debian/changelog +7 −0 Original line number Diff line number Diff line seqan2 (2.4.0+dfsg-9) UNRELEASED; urgency=medium * Generate the CWL descritions automatically, now that CTDConverter is packaged. -- Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 22 Feb 2018 08:19:39 -0800 seqan2 (2.4.0+dfsg-8) unstable; urgency=medium * Fix AutoPkgTests. Miscellaneous cleanups of debian/rules. Loading debian/control +1 −0 Original line number Diff line number Diff line Loading @@ -13,6 +13,7 @@ Build-Depends-Arch: zlib1g-dev, libbam-dev, libboost-dev, help2man, ctdconverter #Build-Depends-Indep: dh-exec #dh-linktree, #python-nose, Loading debian/cwl/alf.cwldeleted 100644 → 0 +0 −119 Original line number Diff line number Diff line #!/usr/bin/env cwl-runner # This CWL file was automatically generated using CTDConverter. # Visit https://github.com/WorkflowConversion/CTDConverter for more information. baseCommand: alf class: CommandLineTool cwlVersion: v1.0 doc: "Compute pairwise similarity of sequences using alignment-free methods in IN.FASTA\ \ and write out tab-delimited matrix with pairwise scores to OUT.TXT.\n\n\n\nFor\ \ more information, visit http://www.seqan.de" inputs: - default: 'false' doc: When given, details about the progress are printed to the screen. id: param_verbose inputBinding: prefix: -verbose label: When given, details about the progress are printed to the screen. type: - 'null' - string - doc: Name of the multi-FASTA input file. id: param_input-file inputBinding: prefix: -input-file label: Name of the multi-FASTA input file. type: File - doc: Filename for output-file output file id: param_output-file_filename inputBinding: prefix: -output-file label: Filename for output-file output file type: - 'null' - string - default: N2 doc: Select method to use. id: param_method inputBinding: prefix: -method label: Select method to use. type: - 'null' - string - default: '4' doc: Size of the k-mers. id: param_k-mer-size inputBinding: prefix: -k-mer-size label: Size of the k-mers. type: - 'null' - int - default: '1' doc: Order of background Markov Model. id: param_bg-model-order inputBinding: prefix: -bg-model-order label: Order of background Markov Model. type: - 'null' - int - default: input doc: Which strand to score. Use both_strands to score both strands simultaneously. id: param_reverse-complement inputBinding: prefix: -reverse-complement label: Which strand to score. Use both_strands to score both strands simultaneously. type: - 'null' - string - default: '0' doc: Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the k-mer-neighbour with one mismatch. id: param_mismatches inputBinding: prefix: -mismatches label: Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the k-mer-neighbour with one mismatch. type: - 'null' - int - default: '0.1' doc: Real-valued weight of counts for words with mismatches. id: param_mismatch-weight inputBinding: prefix: -mismatch-weight label: Real-valued weight of counts for words with mismatches. type: - 'null' - double - doc: Filename for k-mer-weights-file output file id: param_k-mer-weights-file_filename inputBinding: prefix: -k-mer-weights-file label: Filename for k-mer-weights-file output file type: - 'null' - string label: Alignment free sequence comparison outputs: - doc: Name of the file to which the tab-delimtied matrix with pairwise scores will be written to. Default is to write to stdout. id: param_output-file label: Name of the file to which the tab-delimtied matrix with pairwise scores will be written to. Default is to write to stdout. outputBinding: glob: $(inputs.param_output-file_filename) type: - 'null' - File - doc: Print k-mer weights for every sequence to this file if given. id: param_k-mer-weights-file label: Print k-mer weights for every sequence to this file if given. outputBinding: glob: $(inputs.param_k-mer-weights-file_filename) type: - 'null' - File debian/cwl/bam2roi.cwldeleted 100644 → 0 +0 −78 Original line number Diff line number Diff line #!/usr/bin/env cwl-runner # This CWL file was automatically generated using CTDConverter. # Visit https://github.com/WorkflowConversion/CTDConverter for more information. baseCommand: bam2roi class: CommandLineTool cwlVersion: v1.0 doc: "Calculated consecutive regions of coverage from alignment file IN.bam and write\ \ regions of interest to file OUT.roi. Counting is performed over the entire region\ \ (including intron and N-regions) based on the CIGAR string of the alignment record.\n\ \n\n\nFor more information, visit http://www.seqan.de" inputs: - default: 'false' doc: Verbose mode. id: param_verbose inputBinding: prefix: -verbose label: Verbose mode. type: - 'null' - string - default: 'false' doc: Very verbose mode. id: param_very-verbose inputBinding: prefix: -very-verbose label: Very verbose mode. type: - 'null' - string - doc: SAM/BAM formatted file. Must be sorted by coordinate. id: param_input-file inputBinding: prefix: -input-file label: SAM/BAM formatted file. Must be sorted by coordinate. type: File - doc: Filename for output-file output file id: param_output-file_filename inputBinding: prefix: -output-file label: Filename for output-file output file type: string - default: 'false' doc: Calculate strand-specific ROIs (see section Strand Specificness below. id: param_strand-specific inputBinding: prefix: -strand-specific label: Calculate strand-specific ROIs (see section Strand Specificness below. type: - 'null' - string - default: 'false' doc: Ignore paired information. Also see Section ROI Creation Details. id: param_ignore-pairing inputBinding: prefix: -ignore-pairing label: Ignore paired information. Also see Section ROI Creation Details. type: - 'null' - string - default: 'false' doc: Link over skipped bases in the read alignment. id: param_link-over-skipped inputBinding: prefix: -link-over-skipped label: Link over skipped bases in the read alignment. type: - 'null' - string label: Create ROI from BAM file. outputs: - doc: Output file with regions of interest. id: param_output-file label: Output file with regions of interest. outputBinding: glob: $(inputs.param_output-file_filename) type: File Loading
debian/README.sourcedeleted 100644 → 0 +0 −4 Original line number Diff line number Diff line The cwl/ directory was generated thusly: All binaries were called with --write-ctd and those CTDs were converted to CWL using https://github.com/WorkflowConversion/CTDConverter
debian/changelog +7 −0 Original line number Diff line number Diff line seqan2 (2.4.0+dfsg-9) UNRELEASED; urgency=medium * Generate the CWL descritions automatically, now that CTDConverter is packaged. -- Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 22 Feb 2018 08:19:39 -0800 seqan2 (2.4.0+dfsg-8) unstable; urgency=medium * Fix AutoPkgTests. Miscellaneous cleanups of debian/rules. Loading
debian/control +1 −0 Original line number Diff line number Diff line Loading @@ -13,6 +13,7 @@ Build-Depends-Arch: zlib1g-dev, libbam-dev, libboost-dev, help2man, ctdconverter #Build-Depends-Indep: dh-exec #dh-linktree, #python-nose, Loading
debian/cwl/alf.cwldeleted 100644 → 0 +0 −119 Original line number Diff line number Diff line #!/usr/bin/env cwl-runner # This CWL file was automatically generated using CTDConverter. # Visit https://github.com/WorkflowConversion/CTDConverter for more information. baseCommand: alf class: CommandLineTool cwlVersion: v1.0 doc: "Compute pairwise similarity of sequences using alignment-free methods in IN.FASTA\ \ and write out tab-delimited matrix with pairwise scores to OUT.TXT.\n\n\n\nFor\ \ more information, visit http://www.seqan.de" inputs: - default: 'false' doc: When given, details about the progress are printed to the screen. id: param_verbose inputBinding: prefix: -verbose label: When given, details about the progress are printed to the screen. type: - 'null' - string - doc: Name of the multi-FASTA input file. id: param_input-file inputBinding: prefix: -input-file label: Name of the multi-FASTA input file. type: File - doc: Filename for output-file output file id: param_output-file_filename inputBinding: prefix: -output-file label: Filename for output-file output file type: - 'null' - string - default: N2 doc: Select method to use. id: param_method inputBinding: prefix: -method label: Select method to use. type: - 'null' - string - default: '4' doc: Size of the k-mers. id: param_k-mer-size inputBinding: prefix: -k-mer-size label: Size of the k-mers. type: - 'null' - int - default: '1' doc: Order of background Markov Model. id: param_bg-model-order inputBinding: prefix: -bg-model-order label: Order of background Markov Model. type: - 'null' - int - default: input doc: Which strand to score. Use both_strands to score both strands simultaneously. id: param_reverse-complement inputBinding: prefix: -reverse-complement label: Which strand to score. Use both_strands to score both strands simultaneously. type: - 'null' - string - default: '0' doc: Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the k-mer-neighbour with one mismatch. id: param_mismatches inputBinding: prefix: -mismatches label: Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the k-mer-neighbour with one mismatch. type: - 'null' - int - default: '0.1' doc: Real-valued weight of counts for words with mismatches. id: param_mismatch-weight inputBinding: prefix: -mismatch-weight label: Real-valued weight of counts for words with mismatches. type: - 'null' - double - doc: Filename for k-mer-weights-file output file id: param_k-mer-weights-file_filename inputBinding: prefix: -k-mer-weights-file label: Filename for k-mer-weights-file output file type: - 'null' - string label: Alignment free sequence comparison outputs: - doc: Name of the file to which the tab-delimtied matrix with pairwise scores will be written to. Default is to write to stdout. id: param_output-file label: Name of the file to which the tab-delimtied matrix with pairwise scores will be written to. Default is to write to stdout. outputBinding: glob: $(inputs.param_output-file_filename) type: - 'null' - File - doc: Print k-mer weights for every sequence to this file if given. id: param_k-mer-weights-file label: Print k-mer weights for every sequence to this file if given. outputBinding: glob: $(inputs.param_k-mer-weights-file_filename) type: - 'null' - File
debian/cwl/bam2roi.cwldeleted 100644 → 0 +0 −78 Original line number Diff line number Diff line #!/usr/bin/env cwl-runner # This CWL file was automatically generated using CTDConverter. # Visit https://github.com/WorkflowConversion/CTDConverter for more information. baseCommand: bam2roi class: CommandLineTool cwlVersion: v1.0 doc: "Calculated consecutive regions of coverage from alignment file IN.bam and write\ \ regions of interest to file OUT.roi. Counting is performed over the entire region\ \ (including intron and N-regions) based on the CIGAR string of the alignment record.\n\ \n\n\nFor more information, visit http://www.seqan.de" inputs: - default: 'false' doc: Verbose mode. id: param_verbose inputBinding: prefix: -verbose label: Verbose mode. type: - 'null' - string - default: 'false' doc: Very verbose mode. id: param_very-verbose inputBinding: prefix: -very-verbose label: Very verbose mode. type: - 'null' - string - doc: SAM/BAM formatted file. Must be sorted by coordinate. id: param_input-file inputBinding: prefix: -input-file label: SAM/BAM formatted file. Must be sorted by coordinate. type: File - doc: Filename for output-file output file id: param_output-file_filename inputBinding: prefix: -output-file label: Filename for output-file output file type: string - default: 'false' doc: Calculate strand-specific ROIs (see section Strand Specificness below. id: param_strand-specific inputBinding: prefix: -strand-specific label: Calculate strand-specific ROIs (see section Strand Specificness below. type: - 'null' - string - default: 'false' doc: Ignore paired information. Also see Section ROI Creation Details. id: param_ignore-pairing inputBinding: prefix: -ignore-pairing label: Ignore paired information. Also see Section ROI Creation Details. type: - 'null' - string - default: 'false' doc: Link over skipped bases in the read alignment. id: param_link-over-skipped inputBinding: prefix: -link-over-skipped label: Link over skipped bases in the read alignment. type: - 'null' - string label: Create ROI from BAM file. outputs: - doc: Output file with regions of interest. id: param_output-file label: Output file with regions of interest. outputBinding: glob: $(inputs.param_output-file_filename) type: File
