diff --git a/Docker/L570745_uv_first10.MS.tar.xz b/Docker/L570745_uv_first10.MS.tar.xz
new file mode 100644
index 0000000000000000000000000000000000000000..13ab4c559979bdb321d6bdf57d92f03bb84ca2f2
--- /dev/null
+++ b/Docker/L570745_uv_first10.MS.tar.xz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d6acef40bcf795c5ae94232654414fece4a20eb75494577ea630fc663673b3c1
+size 387119976
diff --git a/Docker/test_data/.gitattributes b/Docker/test_data/.gitattributes
deleted file mode 100644
index 8089a9bc54f7507aa1dad9ba738e3a8e0b922f98..0000000000000000000000000000000000000000
--- a/Docker/test_data/.gitattributes
+++ /dev/null
@@ -1 +0,0 @@
-*.h5 filter=lfs diff=lfs merge=lfs -text
\ No newline at end of file
diff --git a/Docker/test_data/example.h5 b/Docker/test_data/example.h5
index 4189e836347c25306c773352d9a0ecc16310a959..554933b577a0dcf1b2aa3fa91c7de5b2477fd724 100644
Binary files a/Docker/test_data/example.h5 and b/Docker/test_data/example.h5 differ
diff --git a/steps/gaincal.cwl b/steps/gaincal.cwl
index d57b71284e6dbbb7c8068f505c3d0b00b97d1868..5b1f47559b12511e51662ec8330dd7a4ffd077f4 100644
--- a/steps/gaincal.cwl
+++ b/steps/gaincal.cwl
@@ -1,119 +1,171 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
+$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
+ sbg: 'https://www.sevenbridges.com/'
id: gaincal
-baseCommand: [DPPP]
-
-requirements:
- InlineJavascriptRequirement: {}
-
-hints:
- DockerRequirement:
- dockerPull: lofareosc/lofar-pipeline-ci:latest
-
-arguments:
- - steps=[gaincal]
-
-
+baseCommand:
+ - DPPP
inputs:
- id: msin
- type: Directory?
- doc: Input Measurement Set
+ type: Directory
inputBinding:
- prefix: msin=
- separate: false
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
- id: caltype
+ type:
+ type: enum
+ symbols:
+ - diagonal
+ - fulljones
+ - phaseonly
+ - scalarphase
+ - amplitude
+ - scalaramplitude
+ - tec
+ - tecandphase
+ name: caltype
+ inputBinding:
+ position: 0
+ prefix: gaincal.caltype=
+ separate: false
doc: |
The type of calibration that needs to be performed.
- type:
- type: enum
- symbols:
- - diagonal
- - fulljones
- - phaseonly
- - scalarphase
- - amplitude
- - scalaramplitude
- - tec
- - tecandphase
- inputBinding:
- prefix: gaincal.caltype=
- separate: false
+ - default: instrument.h5
+ id: output_name_h5parm
+ type: string
+ inputBinding:
+ position: 0
+ prefix: gaincal.parmdb=
+ separate: false
+ - id: blrange
+ type: 'string[]?'
+ inputBinding:
+ position: 0
+ prefix: gaincal.blrange=
+ separate: false
+ itemSeparator: ','
+ valueFrom: '[$(self)]'
+ doc: Vector of baseline lengths to use for calibration
+ - id: uvlambdamin
+ type: float?
+ inputBinding:
+ position: 0
+ prefix: gaincal.uvlambdamin=
+ separate: false
+ - id: baseline
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: gaincal.baseline=
+ separate: false
+ - id: applysolutions
+ type: boolean?
+ doc: Apply the calibration solution to the visibilities. Note that you should always also inspect the parmdb afterwards to check that the solutions look reasonable.
+ inputBinding:
+ prefix: gaincal.applysolutions=
+ - id: solint
+ default: 1
+ type: int
+ doc: >
+ Number of time slots on which a solution is assumed to be constant (same
+ as CellSize.Time in BBS).
+
+ 0 means all time slots. Note that for larger settings of solint, and
+ specially for solint = 0,
+
+ the memory usage of gaincal will be large (all visibilities for a solint
+ should fit in memory).
+ - id: nchan
+ type: int
+ inputBinding:
+ position: 0
+ prefix: gaincal.nchan=
+ separate: false
+
- id: sourcedb
type: File
inputBinding:
- prefix: gaincal.sourcedb=
- separate: false
- - id: usebeammodel
+ position: 0
+ prefix: gaincal.sourcedb=
+ separate: false
+ - id: usemodelcolumn
+ default: MODEL_DATA
+ type: boolean?
+ inputBinding:
+ position: 0
+ prefix: gaincal.usemodelcolumn=
+ separate: false
+ doc: "\tUse model column. The model column name can be specified with msin.modelcolumn\n"
+ - default: true
+ id: usebeammodel
type: boolean
- default: true
inputBinding:
- prefix: gaincal.usebeammodel=true
- separate: false
- - id: storagemanager
+ position: 0
+ prefix: gaincal.usebeammodel=true
+ separate: false
+ - default: dysco
+ id: storagemanager
type: string
- default: dysco
- inputBinding
+ inputBinding:
+ position: 0
prefix: msout.storagemanager=
- - id: solint
- type: int
- default: 1
- doc: |
- Number of time slots on which a solution is assumed to be constant (same as CellSize.Time in BBS).
- 0 means all time slots. Note that for larger settings of solint, and specially for solint = 0,
- the memory usage of gaincal will be large (all visibilities for a solint should fit in memory).
- - id: msin_datacolumn
+ - default: DATA
+ id: msin_datacolumn
type: string?
- default: DATA
- doc: Input data Column
inputBinding:
- prefix: msin.datacolumn=
- separate: false
- - id: onebeamperpatch
- type: boolean
+ position: 0
+ prefix: msin.datacolumn=
+ separate: false
doc: Input data Column
- default: true
+ - default: true
+ id: onebeamperpatch
+ type: boolean
inputBinding:
- prefix: gaincal.onebeamperpatch=True
- separate: false
- - id: msin_modelcolum
+ position: 0
+ prefix: gaincal.onebeamperpatch=True
+ separate: false
+ doc: Input data Column
+ - default: MODEL_DATA
+ id: msin_modelcolum
type: string
- default: MODEL_DATA
- doc: Model data Column
inputBinding:
- prefix: msin.modelcolumn=
- separate: false
-
- - id: output_name_h5parm
+ position: 0
+ prefix: msin.modelcolumn=
+ separate: false
+ doc: Model data Column
+ - default: out.MS
+ id: msout_name
type: string
- default: instrument.h5
inputBinding:
- prefix: gaincal.parmdb=
- separate: false
- - id: msout_name
- type: string
+ position: 0
+ prefix: msout=
+ separate: false
doc: Output Measurement Set
- default: out.MS
+ - id: input
+ type: File?
inputBinding:
- prefix: msout=
- separate: false
-
+ position: 0
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
- glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
-
+ glob: '$(inputs.msout_name=="."?inputs.msin:inputs.msout_name)'
- id: h5parm
doc: Filename of output H5Parm (to be read by e.g. losoto)
type: File
- format: lofar:#H5Parm
outputBinding:
glob: $(inputs.output_name_h5parm)
-
-$namespaces:
- lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+ format: 'lofar:#H5Parm'
+arguments:
+ - 'steps=[gaincal]'
+hints:
+ - class: DockerRequirement
+ dockerPull: 'lofareosc/lofar-pipeline:latest'
+requirements:
+ - class: InlineJavascriptRequirement
$schema:
- - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/test_data/.gitattributes b/test_data/.gitattributes
deleted file mode 100644
index 8089a9bc54f7507aa1dad9ba738e3a8e0b922f98..0000000000000000000000000000000000000000
--- a/test_data/.gitattributes
+++ /dev/null
@@ -1 +0,0 @@
-*.h5 filter=lfs diff=lfs merge=lfs -text
\ No newline at end of file
diff --git a/test_data/L570745_uv_first10.MS.tar.xz b/test_data/L570745_uv_first10.MS.tar.xz
new file mode 100644
index 0000000000000000000000000000000000000000..13ab4c559979bdb321d6bdf57d92f03bb84ca2f2
--- /dev/null
+++ b/test_data/L570745_uv_first10.MS.tar.xz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d6acef40bcf795c5ae94232654414fece4a20eb75494577ea630fc663673b3c1
+size 387119976
diff --git a/test_data/example.h5 b/test_data/example.h5
index 4189e836347c25306c773352d9a0ecc16310a959..554933b577a0dcf1b2aa3fa91c7de5b2477fd724 100644
Binary files a/test_data/example.h5 and b/test_data/example.h5 differ