MaskPrimers.py.cwl in progress

Author: johnfonner

tools/pRESTO/MaskPrimers.py.cwl

@@ -0,0 +1,100 @@
+class: CommandLineTool
+id: MaskPrimers.py
+label: pRESTO MaskPrimers.py
+
+description: |
+  usage: MaskPrimers.py [-h] [-v]  ...
+  
+  Removes primers and annotates sequences with primer and barcode identifiers
+  
+  optional arguments:
+    -h, --help     show this help message and exit
+    -v, --version  show program's version number and exit
+  
+  subcommands:
+                   Alignment method
+      align        Find primer matches using pairwise local alignment
+      score        Find primer matches by scoring primers at a fixed position
+  
+  output files:
+    mask-pass      processed reads with successful primer matches.
+    mask-fail      raw reads failing primer identification.
+  
+  output annotation fields:
+    SEQORIENT      the orientation of the output sequence. Either F (input)
+                   or RC (reverse complement of input).
+    PRIMER         name of the best primer match.
+    BARCODE        the sequence preceding the primer match. Only output when
+                   the --barcode flag is specified.
+  
+requirements:
+
+inputs:
+  - id: "#subcommand"
+    type: enum
+    symbols: ["score", "align"]
+    inputBinding:
+      position: 0 
+
+  - id: "#input_files"
+    type: File 
+    inputBinding:
+      prefix: "-s"
+
+  - id: "#primer_file"
+    type: File 
+    inputBinding:
+      prefix: "-p"
+
+  - id: "#mode"
+    type: enum
+    symbols: ["cut","mask","trim","tag"]
+    inputBinding:
+      prefix: "--mode"
+
+  - id: "#barcode"
+    type: boolean
+    inputBinding:
+      prefix: "--barcode"
+
+  - id: "#start"
+    type: int
+    inputBinding:
+      prefix: "--start"
+
+  - id: "#maxerror"
+    type: float
+    inputBinding:
+      prefix: "--maxerror"
+
+  - id: "#nproc"
+    type: int
+    inputBinding:
+      prefix: "--nproc"
+
+  - id: "#outname"
+    type: string
+    inputBinding:
+      prefix: "--outname"
+
+  - id: "#outdir"
+    type: string
+    inputBinding:
+      prefix: "--outdir"
+
+  - id: "#pipeline_log"
+    type: string
+    inputBinding:
+      prefix: "--outdir"
+
+  - id: "#error_log"
+    type: string
+    inputBinding:
+      prefix: "--outdir"
+
+
+outputs:
+  - id: "#outputs"
+    type: 
+
+# _primers-pass.fastq