diff pilon.cwl @ 0:eaf4a7ae3a8f draft

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pilon.cwl	Thu Aug 11 06:56:35 2016 -0400
@@ -0,0 +1,322 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+stdout: output.txt
+
+requirements:
+  - class: EnvVarRequirement
+    envDef:
+      - envName: CLASSPATH
+        envValue: /home/pvh/Documents/code/SANBI/pilon/pilon-1.18.jar
+#  - class: InlineJavascriptRequirement
+
+inputs:
+  java_opts:
+    type: string?
+    doc: "JVM arguments should a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")"
+    inputBinding:
+      position: 1
+  genome:
+    type: File
+    doc: |
+      The input genome we are trying to improve, which must be the reference used
+      for the bam alignments.  At least one of --frags or --jumps must also be given.
+    inputBinding:
+      position: 5
+      prefix: "--genome"
+  frags:
+    type:
+      - 'null'
+      - type: array
+        items: File
+        inputBinding:
+          prefix: --frags
+          position: 6
+    doc: |
+      A bam file consisting of fragment paired-end alignments, aligned to the --genome
+      argument using bwa or bowtie2.  This argument may be specifed more than once.
+    secondaryFiles:
+      - ".bai"
+  jumps:
+    type:
+      - 'null'
+      - type: array
+        items: File
+        inputBinding:
+          prefix: --jumps
+          position: 6
+    doc: |
+      A bam file consisting of fragment paired-end alignments, aligned to the --genome
+      argument using bwa or bowtie2.  This argument may be specifed more than once.
+    secondaryFiles:
+      - ".bai"
+  unpaired:
+    type:
+      - 'null'
+      - type: array
+        items: File
+        inputBinding:
+          prefix: --unpaired
+          position: 6
+    doc: |
+      A bam file consisting of unpaired alignments, aligned to the --genome argument
+      using bwa or bowtie2.  This argument may be specifed more than once.
+    secondaryFiles:
+      - ".bai"
+  bam:
+    type:
+      - 'null'
+      - type: array
+        items: File
+        inputBinding:
+          prefix: "--bam"
+          position: 6
+    secondaryFiles:
+      - ".bai"
+    doc: |
+      A bam file of unknown type; Pilon will scan it and attempt to classify it as one
+      of the above bam types.
+  vcf_output:
+    type: boolean
+    default: false
+    inputBinding:
+      position: 7
+      prefix: "--vcf"
+  output_prefix:
+    type: string
+    default: pilon
+    inputBinding:
+      prefix: "--output"
+      position: 7
+  variant_output:
+    type: boolean
+    default: false
+    doc: Sets up heuristics for variant calling, as opposed to assembly improvement, equivalent to "--vcf --fix all,breaks"
+    inputBinding:
+      prefix: --variant
+      position: 7
+  changes:
+    type: boolean
+    default: false
+    doc: Output file describing changes in FASTA output
+    inputBinding:
+      prefix: --changes
+      position: 7
+  tracks:
+    type: boolean
+    default: false
+    doc: Write many track files (*.bed, *.wig) suitable for viewing in a genome browser.
+    inputBinding:
+      prefix: --tracks
+      position: 7
+  vcfqe:
+    type: boolean
+    default: false
+    doc: Add a QE (quality-weighted evidence) field rather than the default QP (quality-weighted percentage of evidence) field.
+    inputBinding:
+      prefix: --vcfqe
+      position: 7
+  chunksize:
+    type: int?
+    doc: Input FASTA elements larger than this will be processed in smaller pieces not to exceed this size (default 10000000).
+    inputBinding:
+      prefix: --chunksize
+      position: 8
+  vcf:
+    type: boolean
+    default: false
+    doc: Generate a VCF file describing variants
+    inputBinding:
+      prefix: --vcf
+      position: 8
+  diploid:
+    type: boolean
+    default: false
+    doc: Sample is from diploid organism; will eventually affect calling of heterozygous SNPs
+    inputBinding:
+      prefix: --diploid
+      position: 8
+  fix:
+    type: string?
+    doc: |
+              A comma-separated list of categories of issues to try to fix:
+                "bases": try to fix individual bases and small indels;
+                "gaps": try to fill gaps;
+                "local": try to detect and fix local misassemblies;
+                "all": all of the above (default);
+                "none": none of the above; new fasta file will not be written.
+              The following are experimental fix types:
+                "amb": fix ambiguous bases in fasta output (to most likely alternative).
+                "breaks": allow local reassembly to open new gaps (with "local").
+                "novel": assemble novel sequence from unaligned non-jump reads.
+    inputBinding:
+      prefix: --fix
+      position: 8
+  dumpreads:
+    type: boolean
+    default: false
+    doc: Dump reads for local re-assemblies.
+    inputBinding:
+      prefix: --dumpreads
+      position: 8
+  duplicates:
+    type: boolean
+    default: false
+    doc: Use reads marked as duplicates in the input BAMs (ignored by default).
+    inputBinding:
+      prefix: --duplicates
+      position: 8
+  iupac:
+    type: boolean
+    default: false
+    doc: Output IUPAC ambiguous base codes in the output FASTA file when appropriate.
+    inputBinding:
+      prefix: --iupac
+      position: 8
+  nonpf:
+    type: boolean
+    default: false
+    doc: Use reads which failed sequencer quality filtering (ignored by default).
+    inputBinding:
+      prefix: --nonpf
+      position: 8
+  targets:
+    type: string?
+    doc: |
+      Only process the specified target(s).  Targets are comma-separated, and each target
+      is a fasta element name optionally followed by a base range.
+      Example: "scaffold00001,scaffold00002:10000-20000" would result in processing all of
+      scaffold00001 and coordinates 10000-20000 of scaffold00002.
+      If "targetlist" is the name of a file, each line will be treated as a target
+      specification.
+    inputBinding:
+      prefix: --targets
+      position: 8
+  threads:
+    type: int?
+    doc: Degree of parallelism to use for certain processing (default 1). Experimental.
+    default: 1
+    inputBinding:
+      prefix: --threads
+      position: 8
+  verbose:
+    type: boolean
+    default: false
+    doc: More verbose output
+    inputBinding:
+      prefix: --verbose
+      position: 8
+  debug:
+    type: boolean
+    default: false
+    doc: Debugging output (implies verbose)
+    inputBinding:
+      prefix: --debug
+      position: 8
+  defaultqual:
+    type: int?
+    doc: Assumes bases are of this quality if quals are no present in input BAMs (default 15).
+    inputBinding:
+      prefix: --defaultqual
+      position: 9
+  flank:
+    type: int?
+    doc: Controls how much of the well-aligned reads will be used; this many bases at each end of the good reads will be ignored (default 10).
+    inputBinding:
+      prefix: --flank
+      position: 9
+  gapmargin:
+    type: int?
+    doc: Closed gaps must be within this number of bases of true size to be closed (100000)
+    inputBinding:
+      prefix: --gapmargin
+      position: 9
+  kmersize:
+    type: int?
+    doc: Kmer size used by internal assembler (default 47).
+    inputBinding:
+      prefix: --K
+      position: 9
+  mindepth:
+    type: float?
+    doc: |
+      Variants (snps and indels) will only be called if there is coverage of good pairs
+      at this depth or more; if this value is >= 1, it is an absolute depth, if it is a
+      fraction < 1, then minimum depth is computed by multiplying this value by the mean
+      coverage for the region, with a minumum value of 5 (default 0.1: min depth to call
+      is 10% of mean coverage or 5, whichever is greater).
+    inputBinding:
+      prefix: --mindepth
+      position: 9
+  mingap:
+    type: int?
+    doc: Minimum size for unclosed gaps (default 10)
+    inputBinding:
+      prefix: --mingap
+      position: 9
+  minmq:
+    type: int?
+    doc: Minimum alignment mapping quality for a read to count in pileups (default 0)
+    inputBinding:
+      prefix: --minmq
+      position: 9
+  minqual:
+    type: int?
+    doc: Minimum base quality to consider for pileups (default 0)
+    inputBinding:
+      prefix: --minqual
+      position: 9
+  nostrays:
+    type: boolean
+    default: false
+    doc: |
+      Skip making a pass through the input BAM files to identify stray pairs, that is,
+      those pairs in which both reads are aligned but not marked valid because they have
+      inconsistent orientation or separation. Identifying stray pairs can help fill gaps
+      and assemble larger insertions, especially of repeat content.  However, doing so
+      sometimes consumes considerable memory.
+    inputBinding:
+      prefix: --nostrays
+      position: 9
+
+outputs:
+  pilon_output:
+    type: stdout
+  fasta_output:
+    type: File?
+    outputBinding:
+      glob: $(inputs.output_prefix).fasta
+  vcf_output:
+    type: File?
+    outputBinding:
+      glob: $(inputs.output_prefix).vcf
+  track_outputs:
+    type: File[]?
+    outputBinding:
+      glob:
+        - $(inputs.output_prefix)Pilon.bed
+        - $(inputs.output_prefix)Changes.wig
+        - $(inputs.output_prefix)Unconfirmed.wig
+        - $(inputs.output_prefix)CopyNumber.wig
+        - $(inputs.output_prefix)Coverage.wig
+        - $(inputs.output_prefix)BadCoverage.wig
+        - $(inputs.output_prefix)PctBad.wig
+        - $(inputs.output_prefix)DeltaCoverage.wig
+        - $(inputs.output_prefix)DipCoverage.wig
+        - $(inputs.output_prefix)PhysicalCoverage.wig
+        - $(inputs.output_prefix)ClippedAlignments.wig
+        - $(inputs.output_prefix)WeightedQual.wig
+        - $(inputs.output_prefix)WeightedMq.wig
+        - $(inputs.output_prefix)GC.wig
+
+  changes_output:
+    type: File?
+    outputBinding:
+      glob: $(inputs.output_prefix).changes
+
+baseCommand: [java]
+
+arguments:
+    - valueFrom: "com.simontuffs.onejar.Boot"
+      position: 2