From 6cab2d64bd7f38b0afe2e7ce78689bc92ae99e95 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Wed, 2 Oct 2019 10:55:51 +0200
Subject: [PATCH] Refactor naming and clean up old files
---
...tor.cwl => DP3.AOFlaggerStepGenerator.cwl} | 0
...ator.cwl => DP3.AveragerStepGenerator.cwl} | 0
...rator.cwl => DP3.DemixerStepGenerator.cwl} | 0
...rator.cwl => DP3.EmptyParsetGenerator.cwl} | 0
...setselector.cwl => DP3.ParsetSelector.cwl} | 2 +
steps/DP3.PreflaggerStepGenerator.cwl | 306 ++++++++++++++++++
steps/DP3_flag_averaging.cwl | 123 -------
steps/{DPPPStep.cwl => DPPP.cwl} | 0
steps/GenericParsetGeneratorStep.cwl | 42 ---
steps/PreflaggingStepGenerator.cwl | 236 --------------
steps/check_ateam_separation.cwl | 2 +
steps/echo.cwl | 12 -
...ke_sourcedb_ateam.cwl => makesourcedb.cwl} | 2 +
subworkflow/ndppp_prep_cal.cwl | 24 +-
14 files changed, 325 insertions(+), 424 deletions(-)
rename steps/{AOFlaggerStepGenerator.cwl => DP3.AOFlaggerStepGenerator.cwl} (100%)
rename steps/{AveragingStepGenerator.cwl => DP3.AveragerStepGenerator.cwl} (100%)
rename steps/{DemixingStepGenerator.cwl => DP3.DemixerStepGenerator.cwl} (100%)
rename steps/{EmptyParsetGenerator.cwl => DP3.EmptyParsetGenerator.cwl} (100%)
rename steps/{parsetselector.cwl => DP3.ParsetSelector.cwl} (96%)
mode change 100644 => 100755
create mode 100755 steps/DP3.PreflaggerStepGenerator.cwl
delete mode 100644 steps/DP3_flag_averaging.cwl
rename steps/{DPPPStep.cwl => DPPP.cwl} (100%)
delete mode 100755 steps/GenericParsetGeneratorStep.cwl
delete mode 100755 steps/PreflaggingStepGenerator.cwl
mode change 100644 => 100755 steps/check_ateam_separation.cwl
delete mode 100644 steps/echo.cwl
rename steps/{make_sourcedb_ateam.cwl => makesourcedb.cwl} (97%)
mode change 100644 => 100755
diff --git a/steps/AOFlaggerStepGenerator.cwl b/steps/DP3.AOFlaggerStepGenerator.cwl
similarity index 100%
rename from steps/AOFlaggerStepGenerator.cwl
rename to steps/DP3.AOFlaggerStepGenerator.cwl
diff --git a/steps/AveragingStepGenerator.cwl b/steps/DP3.AveragerStepGenerator.cwl
similarity index 100%
rename from steps/AveragingStepGenerator.cwl
rename to steps/DP3.AveragerStepGenerator.cwl
diff --git a/steps/DemixingStepGenerator.cwl b/steps/DP3.DemixerStepGenerator.cwl
similarity index 100%
rename from steps/DemixingStepGenerator.cwl
rename to steps/DP3.DemixerStepGenerator.cwl
diff --git a/steps/EmptyParsetGenerator.cwl b/steps/DP3.EmptyParsetGenerator.cwl
similarity index 100%
rename from steps/EmptyParsetGenerator.cwl
rename to steps/DP3.EmptyParsetGenerator.cwl
diff --git a/steps/parsetselector.cwl b/steps/DP3.ParsetSelector.cwl
old mode 100644
new mode 100755
similarity index 96%
rename from steps/parsetselector.cwl
rename to steps/DP3.ParsetSelector.cwl
index ce2ef10f..92814cfd
--- a/steps/parsetselector.cwl
+++ b/steps/DP3.ParsetSelector.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
diff --git a/steps/DP3.PreflaggerStepGenerator.cwl b/steps/DP3.PreflaggerStepGenerator.cwl
new file mode 100755
index 00000000..b72b7db6
--- /dev/null
+++ b/steps/DP3.PreflaggerStepGenerator.cwl
@@ -0,0 +1,306 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: preflagging_step_generator
+baseCommand:
+ - parset_concat.py
+inputs:
+ - id: input_parset
+ type: File
+ inputBinding:
+ position: -1
+ prefix: '--input_parset'
+ - default: average
+ id: step_name
+ type: string
+ inputBinding:
+ position: -1
+ doc: unique name for the step
+ - id: input_secondary_files
+ type: 'File[]'
+ doc: Files other than the input used to process the data
+ - default: false
+ id: count.save
+ type: boolean
+ inputBinding:
+ position: 0
+ prefix: count.save=
+ separate: false
+ doc: >-
+ If true, the flag percentages per frequency are saved to a table with
+ extension .flagfreq and percentages per station to a table with extension
+ .flagstat. The basename of the table is the MS name (without extension)
+ followed by the stepname and extension.
+ - default: ''
+ id: count.path
+ type: string
+ inputBinding:
+ position: 0
+ prefix: count.path=
+ separate: false
+ doc: >-
+ The directory where to create the flag percentages table. If empty, the
+ path of the input MS is used.
+ - default: set
+ id: mode
+ type: string
+ inputBinding:
+ position: 0
+ prefix: mode=
+ separate: false
+ doc: >-
+ Case-insensitive string telling what to do with the flags of the data
+ matching (or not matching) the selection criteria given in the other
+ parameters.
+ - default: ''
+ id: expr
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: expr=
+ separate: false
+ doc: >-
+ Expression of preflagger keyword sets (see above). Operators AND, OR, and
+ NOT are possible (or their equivalents &&,&, ||, |, and !). Parentheses
+ can be used to change precedence order. For example:: c1 and (c2 or c3)
+ - default:
+ id: timeofday
+ type: string
+ inputBinding:
+ position: 0
+ prefix: timeofday=
+ separate: false
+ doc: >-
+ Ranges of UTC time-of-day given as st..end or val+-delta. Each value must
+ be given as 12:34:56.789, 12h34m56.789, or as a value followed by a unit
+ like h, min, or s.
+ - default: '[]'
+ id: abstime
+ type: string
+ inputBinding:
+ position: 0
+ prefix: abstime=
+ separate: false
+ doc: >-
+ Ranges of absolute UTC date/time given as st..end or val+-delta. Each
+ value (except delta) must be given as a date/time in casacore MVTime
+ format, for instance 12-Mar-2010/11:31:00.000. A delta value must be given
+ as a time (for instance 1:30:0 or 20s).
+ - default: '[]'
+ id: reltime
+ type: string
+ inputBinding:
+ position: 0
+ prefix: reltime=
+ separate: false
+ doc: >-
+ Ranges of times (using .. or +-) since the start of the observation. A
+ time can be given like 1:30:0 or 20s.
+ - default: '[]'
+ id: timeslot
+ type: string
+ inputBinding:
+ position: 0
+ prefix: timeslot=
+ separate: false
+ doc: >-
+ Time slot sequence numbers. First time slot is 0. st..end means end
+ inclusive.
+ - default: []
+ id: lst
+ type: 'string[]'
+ inputBinding:
+ position: 0
+ prefix: lst=
+ separate: false
+ doc: >-
+ Ranges of Local Apparent Sidereal Times like 1:30:0 +- 20min. The LST of a
+ time slot is calculated for the array position, thus not per antenna.
+ - default: []
+ id: azimuth
+ type: 'float[]'
+ inputBinding:
+ position: 0
+ prefix: azimuth=
+ separate: false
+ doc: >-
+ Ranges of azimuth angles given as st..end or val+-delta. Each value has to
+ be given as a casacore direction like 12:34:56.789 or 12h34m56.789,
+ 12.34.56.789 or 12d34m56.789, or a value followed by a unit like rad or
+ deg.
+ - id: elevation
+ type: string?
+ inputBinding:
+ position: 0
+ prefix: elevation=
+ separate: false
+ doc: 'Ranges of elevation angles (similar to azimuth). For example:: 0deg..10deg'
+ - default: []
+ id: baseline
+ type: string[]
+ inputBinding:
+ position: 0
+ prefix: baseline=
+ separate: false
+ itemSeparator: ','
+ doc: See Description of baseline selection parameters.
+ - default: ''
+ id: corrtype
+ type: string
+ inputBinding:
+ position: 0
+ prefix: corrtype=
+ separate: false
+ doc: 'Correlation type to match? Must be auto, cross, or an empty string.'
+ - default: -1
+ id: blmin
+ type: float
+ inputBinding:
+ position: 0
+ prefix: blmin=
+ separate: false
+ doc: 'If blmin > 0, baselines with length < blmin meter will match.'
+ - default: -1
+ id: blmax
+ type: float
+ inputBinding:
+ position: 0
+ prefix: blmax=
+ separate: false
+ doc: 'If blmax > 0, baselines with length > blmax meter will match.'
+ - default: -1
+ id: uvmmin
+ type: float
+ inputBinding:
+ position: 0
+ prefix: uvmmin=
+ separate: false
+ doc: >-
+ If uvmmin > 0, baselines with UV-distance < uvmmin meter will match. Note
+ that the UV-distance is the projected baseline length.
+ - default: -1
+ id: uvmmax
+ type: float
+ inputBinding:
+ position: 0
+ prefix: uvmmax=
+ separate: false
+ doc: 'If uvmmax > 0, baselines with UV-distance > uvmmax meter will match.'
+ - default: ''
+ id: freqrange
+ type: string
+ inputBinding:
+ position: 0
+ prefix: freqrange=
+ separate: false
+ doc: >-
+ Channels in the given frequency ranges will match. Each value in the
+ vector is a range which can be given as start..end or start+-delta. A
+ value can be followed by a unit like KHz. If only one value in a range has
+ a unit, the unit is also applied to the other value. If a range has no
+ unit, it defaults to MHz. For example: freqrange=[1.2 .. 1.4 MHz,
+ 1.8MHz+-50KHz] flags channels between 1.2MHz and 1.4MHz and between
+ 1.75MHz and 1.85MHz. The example shows that blanks can be used at will.
+ - default: ''
+ id: chan
+ type: string
+ inputBinding:
+ position: 0
+ prefix: chan=
+ separate: false
+ doc: >-
+ The given channels will match (start counting at 0). Channels exceeding
+ the number of channels are ignored. Similar to msin, it is possible to
+ specify the channels as an expression of nchan. Furthermore, .. can be
+ used to specify ranges. For example: chan=[0..nchan/32-1,
+ 31*nchan/32..nchan-1] to flag the first and last 2 or 8 channels
+ (depending on 64 or 256 channels in the observation).
+ - default: -1e+30
+ id: amplmin
+ type: float
+ inputBinding:
+ position: 0
+ prefix: amplmin=
+ separate: false
+ doc: >-
+ Correlation data with amplitude < amplmin will match. It can be given per
+ correlation. For example, amplmin=[100,,,100] matches data points with XX
+ or YY amplitude < 100. The non-specified amplitudes get the default value.
+ - default: 1e+30
+ id: amplmax
+ type: float
+ inputBinding:
+ position: 0
+ prefix: amplmax=
+ separate: false
+ doc: Correlation data with amplitude > amplmax will match.
+ - default: -1e+30
+ id: phasemin
+ type: float
+ inputBinding:
+ position: 0
+ prefix: phasemin=
+ separate: false
+ doc: Correlation data with phase < phasemin (in radians) will match.
+ - default: 1e+30
+ id: phasemax
+ type: float
+ inputBinding:
+ position: 0
+ prefix: phasemax=
+ separate: false
+ doc: Correlation data with phase > phasemax (in radians) will match.
+ - default: -1e+30
+ id: realmin
+ type: float
+ inputBinding:
+ position: 0
+ prefix: realmin=
+ separate: false
+ doc: Correlation data with real complex part < realmin will match.
+ - default: 1e+30
+ id: realmax
+ type: float
+ inputBinding:
+ position: 0
+ prefix: realmax=
+ separate: false
+ doc: Correlation data with real complex part > realmax will match.
+ - default: -1e+30
+ id: imagmin
+ type: float
+ inputBinding:
+ position: 0
+ prefix: imagmin=
+ separate: false
+ doc: Correlation data with imaginary complex part < imagmin will match.
+ - default: 1e+30
+ id: imagmax
+ type: float
+ inputBinding:
+ position: 0
+ prefix: imagmax=
+ separate: false
+ doc: Correlation data with imaginary complex part > imagmax will match.
+outputs:
+ - id: output_parset
+ doc: Parset output file
+ type: File
+ outputBinding:
+ glob: output_parset
+ streamable: true
+ - id: output_secondary_files
+ doc: files needed to execute the step
+ type: 'File[]'
+ outputBinding:
+ outputEval: $(inputs.input_secondary_files)
+arguments:
+ - preflagger
+requirements:
+ - class: DockerRequirement
+ dockerPull: 'prefactor-utils:latest'
+ - class: InlineJavascriptRequirement
+stdout: output_parset
diff --git a/steps/DP3_flag_averaging.cwl b/steps/DP3_flag_averaging.cwl
deleted file mode 100644
index 7556cc69..00000000
--- a/steps/DP3_flag_averaging.cwl
+++ /dev/null
@@ -1,123 +0,0 @@
-cwlVersion: 1.1
-class: CommandLineTool
-baseCommand: [DPPP]
-
-label: "Flagging and Averaging"
-
-hints:
- DockerRequirements:
- dockerPull: lofaruser/imaging-pipeline
-
-inputs:
- msin:
- type: Directory
-
- msin_data_column:
- type: string
- default: "DATA"
-
- msin_writefullresflag:
- type: boolean
- default: False
-
- msin_baselines:
- type: string
- default: ""
-
- msin_autoweight:
- type: boolean
- default: False
-
- msout_data_column:
- type: string
- default: "DATA"
-
- msout_writefullresflag:
- type: boolean
- default: False
-
- msout_overwrite:
- type: boolean
- default: True
-
- msout_storagemanager:
- type: string
- default: "Dysco"
-
- msout_storagemanager_databitrate:
- type: int
- default: 0
-
- flagger_memory_used:
- type: int
- default: 0
-
- flagger_keep_statistics:
- type: boolean
- default: False
-
- flag_baseline:
- type: string
- default: ""
-
- flag_elevation:
- type: string
- default: "0deg..20deg"
-
- flag_amplitude:
- type: double
- default: 1.e-30
-
- interpolate_windowsize:
- type: int
-
-
- avg_timeresolution:
- type: int
- avg_frequenciesresolution:
- type: int
-
- demixer_baseline:
- type: string
- default: ""
-
- demixer_frequency_steps:
- type: int
- default: 4
-
- demixer_time_steps:
- type: int
- default: 4
-
- demixer_ignore_target:
- type: boolean
- default: False
-
- demixer_target_source:
- type: string
-
- demixer_subtract_sources:
- type: string
-
-
-
-outputs:
-
-
-
-
-ndppp_prep_cal.control.type = dppp
-ndppp_prep_cal.control.max_per_node = {{ num_proc_per_node_limit }}
-ndppp_prep_cal.control.error_tolerance = {{ error_tolerance }}
-ndppp_prep_cal.argument.numthreads = {{ max_dppp_threads }}
-
-ndppp_prep_cal.argument.steps = [{{ initial_flagging }},{{ demix_step }}interp,avg]
-ndppp_prep_cal.argument.flagedge.type = preflagger
-ndppp_prep_cal.argument.flagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1] # we are running on a single subband
-
-ndppp_prep_cal.argument.flagbaseline.type = preflagger
-ndppp_prep_cal.argument.flagamp.type = preflagger
-ndppp_prep_cal.argument.interp.type = interpolate
-ndppp_prep_cal.argument.avg.type = average
-ndppp_prep_cal.argument.flagamp.type = preflagger
-ndppp_prep_cal.argument.demix.type = demixer
diff --git a/steps/DPPPStep.cwl b/steps/DPPP.cwl
similarity index 100%
rename from steps/DPPPStep.cwl
rename to steps/DPPP.cwl
diff --git a/steps/GenericParsetGeneratorStep.cwl b/steps/GenericParsetGeneratorStep.cwl
deleted file mode 100755
index 2c1a342a..00000000
--- a/steps/GenericParsetGeneratorStep.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-class: CommandLineTool
-cwlVersion: v1.0
-id: _generic_parset_generator_step
-baseCommand: [parset_concat.py]
-
-requirements:
- DockerRequirement:
- dockerPull: prefactor-utils:latest
-
-inputs:
- - id: step_name
- type: string
- inputBinding:
- position: 1
- doc: name of the DPPP step
- - id: step_type
- type: string
- inputBinding:
- position: 2
- doc: type of the DPPP step
-
- - id: step_arguments
- type: 'string[]'
- inputBinding:
- position: 3
- doc: List of key=value parameters to pass
-outputs:
- - id: output_parset
- doc: Parset output file
- type: File
- streamable: true
- outputBinding: a_stdout_file
-
- - id: input_secondary_files
- doc: files needed to execute the step
- type: File[]
- outputBinding:
- outputEval: $(inputs.input_secondary_files)
-
-stdout: a_stdout_file
diff --git a/steps/PreflaggingStepGenerator.cwl b/steps/PreflaggingStepGenerator.cwl
deleted file mode 100755
index 6307d168..00000000
--- a/steps/PreflaggingStepGenerator.cwl
+++ /dev/null
@@ -1,236 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-class: CommandLineTool
-cwlVersion: v1.0
-id: average_step_generator
-baseCommand: [parset_concat.py]
-
-requirements:
- DockerRequirement:
- dockerPull: prefactor-utils:latest
-
-arguments: ['preflagger']
-
-inputs:
- - id: input_parset
- type: File
- inputBinding:
- position: -1
- prefix: --input_parset
- - id: step_name
- type: string
- default: average
- doc: unique name for the step
- inputBinding:
- position: -1
- - id: input_secondary_files
- type: File[]
- doc: Files other than the input used to process the data
-
-###############################################################################
-
-
- - id: count.save
- type: boolean
- default: false
- doc: If true, the flag percentages per frequency are saved to a table with extension .flagfreq and percentages per station to a table with extension .flagstat. The basename of the table is the MS name (without extension) followed by the stepname and extension.
- inputBinding:
- prefix: <step>.count.save=
- separate: false
- - id: count.path
- type: string
- default: ''
- doc: The directory where to create the flag percentages table. If empty, the path of the input MS is used.
- inputBinding:
- prefix: count.path=
- separate: false
- - id: mode
- type: string
- default: set
- doc: Case-insensitive string telling what to do with the flags of the data matching (or not matching) the selection criteria given in the other parameters.
- inputBinding:
- prefix: mode=
- separate: false
- - id: expr
- type: string
- default: []
- doc: 'Expression of preflagger keyword sets (see above). Operators AND, OR, and NOT are possible (or their equivalents &&,&, ||, |, and !). Parentheses can be used to change precedence order. For example:: c1 and (c2 or c3)'
- inputBinding:
- prefix: expr=
- separate: false
- - id: timeofday
- type: string
- default: []
- doc: Ranges of UTC time-of-day given as st..end or val+-delta. Each value must be given as 12:34:56.789, 12h34m56.789, or as a value followed by a unit like h, min, or s.
- inputBinding:
- prefix: timeofday=
- separate: false
- - id: abstime
- type: string
- default: '[]'
- doc: Ranges of absolute UTC date/time given as st..end or val+-delta. Each value (except delta) must be given as a date/time in casacore MVTime format, for instance 12-Mar-2010/11:31:00.000. A delta value must be given as a time (for instance 1:30:0 or 20s).
- inputBinding:
- prefix: abstime=
- separate: false
- - id: reltime
- type: string
- default: '[]'
- doc: Ranges of times (using .. or +-) since the start of the observation. A time can be given like 1:30:0 or 20s.
- inputBinding:
- prefix: reltime=
- separate: false
- - id: timeslot
- type: string
- default: '[]'
- doc: Time slot sequence numbers. First time slot is 0. st..end means end inclusive.
- inputBinding:
- prefix: timeslot=
- separate: false
- - id: lst
- type: string[]
- default: []
- doc: Ranges of Local Apparent Sidereal Times like 1:30:0 +- 20min. The LST of a time slot is calculated for the array position, thus not per antenna.
- inputBinding:
- prefix: lst=
- separate: false
- - id: azimuth
- type: float[]
- default: []
- doc: Ranges of azimuth angles given as st..end or val+-delta. Each value has to be given as a casacore direction like 12:34:56.789 or 12h34m56.789, 12.34.56.789 or 12d34m56.789, or a value followed by a unit like rad or deg.
- inputBinding:
- prefix: azimuth=
- separate: false
- - id: elevation
- type: float[]
- default: []
- doc: 'Ranges of elevation angles (similar to azimuth). For example:: 0deg..10deg'
- inputBinding:
- prefix: elevation=
- separate: false
- - id: baseline
- type: string[]
- default: ''
- doc: See Description of baseline selection parameters.
- inputBinding:
- prefix: baseline=
- separate: false
- - id: corrtype
- type: string
- default: ''
- doc: Correlation type to match? Must be auto, cross, or an empty string.
- inputBinding:
- prefix: corrtype=
- separate: false
- - id: blmin
- type: double
- default: -1
- doc: If blmin > 0, baselines with length < blmin meter will match.
- inputBinding:
- prefix: blmin=
- separate: false
- - id: blmax
- type: double
- default: -1
- doc: If blmax > 0, baselines with length > blmax meter will match.
- inputBinding:
- prefix: blmax=
- separate: false
- - id: uvmmin
- type: double
- default: -1
- doc: If uvmmin > 0, baselines with UV-distance < uvmmin meter will match. Note that the UV-distance is the projected baseline length.
- inputBinding:
- prefix: uvmmin=
- separate: false
- - id: uvmmax
- type: double
- default: -1
- doc: If uvmmax > 0, baselines with UV-distance > uvmmax meter will match.
- inputBinding:
- prefix: uvmmax=
- separate: false
- - id: freqrange
- type: string
- default: []
- doc: 'Channels in the given frequency ranges will match. Each value in the vector is a range which can be given as start..end or start+-delta. A value can be followed by a unit like KHz. If only one value in a range has a unit, the unit is also applied to the other value. If a range has no unit, it defaults to MHz. For example: freqrange=[1.2 .. 1.4 MHz, 1.8MHz+-50KHz] flags channels between 1.2MHz and 1.4MHz and between 1.75MHz and 1.85MHz. The example shows that blanks can be used at will.'
- inputBinding:
- prefix: freqrange=
- separate: false
- - id: chan
- type: string
- default: []
- doc: 'The given channels will match (start counting at 0). Channels exceeding the number of channels are ignored. Similar to msin, it is possible to specify the channels as an expression of nchan. Furthermore, .. can be used to specify ranges. For example: chan=[0..nchan/32-1, 31*nchan/32..nchan-1] to flag the first and last 2 or 8 channels (depending on 64 or 256 channels in the observation).'
- inputBinding:
- prefix: chan=
- separate: false
- - id: amplmin
- type: float
- default: -1.e30
- doc: "Correlation data with amplitude < amplmin will match. It can be given per correlation. For example, amplmin=[100,,,100] matches data points with XX or YY amplitude < 100. The non-specified amplitudes get the default value."
- inputBinding:
- prefix: amplmin=
- separate: false
- - id: amplmax
- type: float
- default: 1e+030
- doc: Correlation data with amplitude > amplmax will match.
- inputBinding:
- prefix: amplmax=
- separate: false
- - id: phasemin
- type: float
- default: -1.e30
- doc: Correlation data with phase < phasemin (in radians) will match.
- inputBinding:
- prefix: phasemin=
- separate: false
- - id: phasemax
- type: float
- default: +1.e30
- doc: Correlation data with phase > phasemax (in radians) will match.
- inputBinding:
- prefix: phasemax=
- separate: false
- - id: realmin
- type: float
- default: -1.e30
- doc: Correlation data with real complex part < realmin will match.
- inputBinding:
- prefix: realmin=
- separate: false
- - id: realmax
- type: float
- default: 1.e30
- doc: Correlation data with real complex part > realmax will match.
- inputBinding:
- prefix: realmax=
- separate: false
- - id: imagmin
- type: float
- default: -1.e+30
- doc: Correlation data with imaginary complex part < imagmin will match.
- inputBinding:
- prefix: imagmin=
- separate: false
- - id: imagmax
- type: float
- default: 1.e+30
- doc: Correlation data with imaginary complex part > imagmax will match.
- inputBinding:
- prefix: imagmax=
- separate: false
-
-stdout: output_parset
-outputs:
- - id: output_parset
- doc: Parset output file
- streamable: True
- type: File
- outputBinding:
- glob: output_parset
-
- - id: output_secondary_files
- doc: files needed to execute the step
- type: File[]
- outputBinding:
- outputEval: $(inputs.input_secondary_files)
diff --git a/steps/check_ateam_separation.cwl b/steps/check_ateam_separation.cwl
old mode 100644
new mode 100755
index ed7befcd..bb720da5
--- a/steps/check_ateam_separation.cwl
+++ b/steps/check_ateam_separation.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
class: CommandLineTool
cwlVersion: v1.0
id: check_ateam_separation
diff --git a/steps/echo.cwl b/steps/echo.cwl
deleted file mode 100644
index 8e273f66..00000000
--- a/steps/echo.cwl
+++ /dev/null
@@ -1,12 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-id: echo
-baseCommand:
- - cat
-inputs:
- file:
- type: File
- inputBinding:
- position: 1
-
-outputs: []
\ No newline at end of file
diff --git a/steps/make_sourcedb_ateam.cwl b/steps/makesourcedb.cwl
old mode 100644
new mode 100755
similarity index 97%
rename from steps/make_sourcedb_ateam.cwl
rename to steps/makesourcedb.cwl
index 00a834d9..94be58ac
--- a/steps/make_sourcedb_ateam.cwl
+++ b/steps/makesourcedb.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
diff --git a/subworkflow/ndppp_prep_cal.cwl b/subworkflow/ndppp_prep_cal.cwl
index 2dcb9248..6d5daadb 100644
--- a/subworkflow/ndppp_prep_cal.cwl
+++ b/subworkflow/ndppp_prep_cal.cwl
@@ -1,3 +1,5 @@
+#!/usr/bin/env cwl-runner
+
class: Workflow
cwlVersion: v1.0
id: ndppp_prep_cal
@@ -10,7 +12,7 @@ inputs:
'sbg:x': 612.3626098632812
'sbg:y': -442.8657531738281
- id: elevation_to_flag
- type: float
+ type: string
'sbg:x': 847
'sbg:y': -501.7469482421875
- id: min_amplitude_to_flag
@@ -52,7 +54,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/PreflaggingStepGenerator.cwl
+ run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 1160.802978515625
'sbg:y': -95.15213775634766
- id: flagelev
@@ -70,7 +72,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/PreflaggingStepGenerator.cwl
+ run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 1459.2421875
'sbg:y': -83.970458984375
- id: flagamp
@@ -87,7 +89,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/PreflaggingStepGenerator.cwl
+ run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 1659.302001953125
'sbg:y': -23
- id: empty_parset_generator
@@ -95,7 +97,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/EmptyParsetGenerator.cwl
+ run: ../steps/DP3.EmptyParsetGenerator.cwl
'sbg:x': -187.92431640625
'sbg:y': 35.5892333984375
- id: flagedge
@@ -112,7 +114,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/PreflaggingStepGenerator.cwl
+ run: ../steps/DP3.PreflaggerStepGenerator.cwl
'sbg:x': 53.59375762939453
'sbg:y': -119.96077728271484
- id: aoflag
@@ -131,7 +133,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/AOFlaggerStepGenerator.cwl
+ run: ../steps/DP3.AOFlaggerStepGenerator.cwl
'sbg:x': 357.934326171875
'sbg:y': -129.337890625
- id: demix_select
@@ -151,7 +153,7 @@ steps:
out:
- id: output_secondary_files
- id: output_parset
- run: ../steps/parsetselector.cwl
+ run: ../steps/DP3.ParsetSelector.cwl
label: demix?
'sbg:x': 2144.327392578125
'sbg:y': -22.676969528198242
@@ -165,7 +167,7 @@ steps:
out:
- id: output_parset
- id: output_secondary_files
- run: ../steps/DemixingStepGenerator.cwl
+ run: ../steps/DP3.DemixerStepGenerator.cwl
'sbg:x': 1921.2374267578125
'sbg:y': 62.99578094482422
- id: process_raw_data_select
@@ -185,7 +187,7 @@ steps:
out:
- id: output_secondary_files
- id: output_parset
- run: ../steps/parsetselector.cwl
+ run: ../steps/DP3.ParsetSelector.cwl
label: ParsetSelector
'sbg:x': 572.44970703125
'sbg:y': 38.326629638671875
@@ -200,7 +202,7 @@ steps:
- demix_select/output_secondary_files
out:
- id: msout
- run: ../steps/DPPPStep.cwl
+ run: ../steps/DPPP.cwl
'sbg:x': 2516.561767578125
'sbg:y': -25.858686447143555
requirements:
--
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