Adding CWL files

ncbi · Apr 1, 2019 · 4ba17a6 · 4ba17a6
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diff --git a/bamscale-cov.cwl b/bamscale-cov.cwl
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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: BAMscale-cov
+doc: Calculate coverage of BED coordinates in BAM file(s)
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+hints:
+  - $import: bamscale.yml
+
+inputs:
+  l:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -l
+    doc: |
+      Sequencing type to be used. Can be: single, paired, and auto (default: autodetect)
+  f:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -f
+    doc: |
+      Compute coverage using fragments instead of reads (default: no)
+  s:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -s
+    doc: |
+      Reads need to have same orientation of peaks (default: unstranded)
+  r:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -r
+    doc: |
+      Reads need to have reverse orientation of peaks (default: unstranded)
+  e:
+    type: int?
+    inputBinding:
+      position: 2
+      prefix: -e
+    doc: |
+      Compute sequencing coverage from BAM file quickly using the index (option '0'),
+      or count number of reads by parsing entire BAM file (slower, but more accurate; set to '1' [default])
+  c:
+    type: File?
+    inputBinding:
+      position: 2
+      prefix: -c
+    doc: |
+      Input file with list of chromosomes to blacklist when computing coverage for normalization
+  u:
+    type: int?
+    inputBinding:
+      position: 2
+      prefix: -u
+    doc: |
+      BED file with regions to subtract when computing coverage for normalization
+      These coordinates should not overlap so reads are not counted multiple times
+  q:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -q
+    doc: |
+      Minimum (at least) mapping quality (default: 0)
+  d:
+    type: string?
+    inputBinding:
+      position: 3
+      prefix: -d
+    doc: |
+      Keep duplicated reads (default: no)
+  p:
+    type: string?
+    inputBinding:
+      position: 3
+      prefix: -p
+    doc: |
+      Do not filter un-proper alignments (default: filter)
+  m:
+    type: string?
+    inputBinding:
+      position: 3
+      prefix: -m
+    doc: |
+      Do not remove reads with unmapped pairs
+  g:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -g
+    doc: |
+      Minimum fragment size for read pairs (default: 0)
+  x:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -x
+    doc: |
+      Maximum fragment size for read pairs (default: 2000)
+  w:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -w
+    doc: |
+      Filter reads based on fragment size (default: no)
+  t:
+    type: int?
+    inputBinding:
+      position: 4
+      prefix: -t
+    doc: |
+      No. of threads to use (default: 1)
+  n:
+    type: string
+    inputBinding:
+      position: 4
+      prefix: -n
+    doc: |
+      Output prefix for file names (default: none)
+  bed:
+    type: File
+    inputBinding:
+      position: 5
+      prefix: --bed
+    doc: |
+      Input BED file
+  bam:
+    type:
+      type: array
+      items: File
+      inputBinding:
+        prefix: --bam
+        separate: true
+    secondaryFiles: .bai
+    inputBinding:
+      position: 6
+    doc: |
+      Input BAM file. This can be specified multiple times in case of multiple BAM files
+
+outputs:
+  output:
+    type: File[]
+    outputBinding:
+      glob: $(inputs.n)*
+
+baseCommand: ["BAMscale", "cov"]
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-4108-5982
+    s:email: mailto:[email protected]
+    s:name: Roberto Vera Alvarez
+
+s:codeRepository: https://github.com/ncbi/BAMscale
+s:license: https://spdx.org/licenses/OPL-1.0
+
+$namespaces:
+  s: http://schema.org/
+
+$schemas:
+  - http://schema.org/docs/schema_org_rdfa.html
+
diff --git a/bamscale-scale.cwl b/bamscale-scale.cwl
@@ -0,0 +1,216 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: BAMscale-scale
+doc: Scale one or multiple BAM files
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+hints:
+  - $import: bamscale.yml
+
+inputs:
+  l:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -l
+    doc: |
+      Sequencing type to be used. Can be: single, paired, and auto (default: autodetect)
+  f:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -f
+    doc: |
+      Compute coverage using fragments instead of reads (default: no)
+  a:
+    type: int?
+    inputBinding:
+      position: 1
+      prefix: -a
+    doc: |
+      Fragment size to be used to extend single-end library reads
+  y:
+    type: string?
+    inputBinding:
+      position: 2
+      prefix: -y
+    doc: |
+      Type of normalization. (default: base)
+      If no normalization is needed, set '--scale no' argument, the program will disregard this option.
+      Options:
+        1) reads: No. of mapped reads/fragments
+        2) base: Sum of per-base coverage of reads/fragments
+  k:
+    type: string?
+    inputBinding:
+      position: 2
+      prefix: -k
+    doc: |
+      Method to scale samples together. (default: genome)
+      Options are:
+        1) no: no scaling, just calculate coverage
+        2) smallest: scale reads to smallest library (multiple-samples only)
+        3) genome: scale samples to 1x genome coverage (only possible with 'base' normalization type)
+  r:
+    type: string?
+    inputBinding:
+      position: 1
+      prefix: -r
+    doc: |
+      Operation to perform when scaling samples. Default: scaled
+      Options are:
+        1) scaled: output scaled tracks.
+        2) unscaled: do not scale files in any way.
+        2) log2: log2 transform against first BAM file.
+        3) ratio: coverage ratio against first BAM file.
+        4) subtract: subtract coverage against first BAM file.
+        5) rfd: OK-seq RFD calculation
+  z:
+    type: int?
+    inputBinding:
+      position: 2
+      prefix: -z
+    doc: |
+      Size of bins for output bigWig/bedgraph generation (default: 5)
+  e:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -e
+    doc: |
+      Compute sequencing coverage from BAM file. (default: '1', count reads while parsing BAM)
+      Options are:
+        1) 0: use reads in index (only if normalization is set to 'reads')
+        2) 1: count reads while parsing BAM(s)
+      WARNING: this option is only useful when 'reads' are used for normalization
+  c:
+    type: File?
+    inputBinding:
+      position: 3
+      prefix: -c
+    doc: |
+      Input file with list of chromosomes to blacklist when computing coverage for normalization
+  u:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -u
+    doc: |
+      BED file with regions to subtract when computing coverage for normalization
+      These coordinates should not overlap so reads are not counted multiple times
+  j:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -j
+    doc: |
+      Smoothen signal by calculating mean of N bins flanking both sides of each bin (default: 0)
+      If set to '0', the signal is not smoothened. To turn on specify a value greater than '0'.
+      For replication timing, a good value is to smoothen to 100k bases. If binSize is 100bp, this would be '1000'
+  b:
+    type: int?
+    inputBinding:
+      position: 3
+      prefix: -b
+    doc: |
+      Which tracks should be smoothened when performing smoothening (default: '1' meaning only binned track).
+      Options are:
+        1) 0: Smoothen scaled and transformed tracks (log2, ratio or subtracted)
+        2) 1: Smoothen only the scaled sequencing track
+        3) 2: Smoothen only the transformed (log2, ratio or subtract) track
+  q:
+    type: int?
+    inputBinding:
+      position: 4
+      prefix: -q
+    doc: |
+      Minimum (at least) mapping quality (default: 0)
+  d:
+    type: string?
+    inputBinding:
+      position: 4
+      prefix: -d
+    doc: |
+      Keep duplicated reads (default: no)
+  p:
+    type: string?
+    inputBinding:
+      position: 4
+      prefix: -p
+    doc: |
+      Do not filter un-proper alignments (default: filter)
+  m:
+    type: string?
+    inputBinding:
+      position: 4
+      prefix: -m
+    doc: |
+      Do not remove reads with unmapped pairs
+  g:
+    type: int?
+    inputBinding:
+      position: 4
+      prefix: -g
+    doc: |
+      Minimum fragment size for read pairs (default: 0)
+  x:
+    type: int?
+    inputBinding:
+      position: 4
+      prefix: -x
+    doc: |
+      Maximum fragment size for read pairs (default: 2000)
+  w:
+    type: int?
+    inputBinding:
+      position: 4
+      prefix: -w
+    doc: |
+      Filter reads based on fragment size (default: no)
+  t:
+    type: int?
+    inputBinding:
+      position: 5
+      prefix: -t
+    doc: |
+      No. of threads to use (default: 1)
+  bam:
+    type:
+      type: array
+      items: File
+      inputBinding:
+        prefix: --bam
+        separate: true
+    secondaryFiles: .bai
+    inputBinding:
+      position: 6
+    doc: |
+      Input BAM file. This can be specified multiple times in case of multiple BAM files
+
+outputs:
+  output:
+    type: File[]
+    outputBinding:
+       glob: "*.bw"
+
+baseCommand: ["BAMscale", "scale"]
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-4108-5982
+    s:email: mailto:[email protected]
+    s:name: Roberto Vera Alvarez
+
+s:codeRepository: https://github.com/ncbi/BAMscale
+s:license: https://spdx.org/licenses/OPL-1.0
+
+$namespaces:
+  s: http://schema.org/
+
+$schemas:
+  - http://schema.org/docs/schema_org_rdfa.html
+
diff --git a/bamscale.yml b/bamscale.yml
@@ -0,0 +1,4 @@
+  class: DockerRequirement
+  dockerImageId: bamscale
+  dockerFile:
+    $include: https://raw.githubusercontent.com/ncbi/BAMscale/master/Dockerfile