Work in progress: CWL tool descriptions

tools/phenomenal/ms/camera/camera-annotate-peaks.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: CAMERA Annotate Peaks
+
+hints:
+  DockerRequirement:
+    dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
+  SoftwareRequirement:
+    packages:
+      camera:
+        specs:
+          - https://bio.tools/camera
+          - https://identifiers.org/rrid/RRID:SCR_002466
+
+inputs:
+  camera_annotate_peaks:
+    type: File
+    format: iana:application/x-r-data 
+    label: XCMS-Set file
+    doc: A rdata file with a XCMS-Set object from one sample
+
+outputs:
+  peaktable:
+    type: File
+    format: 
+    doc: A rdata file containing one xsAnnotate object 
+    outputBinding:
+      glob: ouput.Rdata
+
+baseCommand: xsAnnotate.r
+
+arguments:
+ - input=$(inputs.camera_annotate_peaks.path)
+ - output=output.Rdata
+
+doc: |
+  Generate xsAnnotate object used for further CAMERA processing
+
+  This module deals with the construction of an xsAnnotate object. It extracts
+  the peaktable from a provided XCMS-Set, which is used for all further
+  analysis. Multiple XCMS-Set objects which were grouped by
+  **xcms-collect-peaks** need to be split by **xcmssplit** beforehand.
+
+  **Please cite**: 
+  R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
+
+  **References**
+  Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
+  an integrated strategy for compound spectra extraction and annotation of
+  liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
+  pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g.
+
+$namespaces: 
+  iana: "https://www.iana.org/assignments/media-types/" 

tools/phenomenal/ms/camera/camera-find-adducts.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: CAMERA Find Adducts
+
+hints:
+  DockerRequirement:
+    dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
+  SoftwareRequirement:
+    packages:
+      camera:
+        specs:
+          - https://bio.tools/camera
+          - https://identifiers.org/rrid/RRID:SCR_002466
+
+inputs:
+  xs_annotate:
+    type: File
+    format: iana:application/x-r-data
+    label: xsAnnotate file
+    doc: A rdata file with a xsAnnotate object from one sample
+  ppm:
+    type: float
+    label: The ppm error for the search
+  polarity:
+    type: string
+    label: Polarity mode used for measuring of the MS sample
+    doc: "Allowed values: positive, negative"
+  rules:
+    type: string
+    label: Adduct ruleset to be used
+    doc: |
+      Allowed values:
+       - primary - contains most common adduct types
+         ([M-H]-, [M-2H+Na]-, [M-2H+K]-, [M+Cl]-, [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+)
+       - extended - next to primary also additional adduct types 
+
+outputs:
+  peak_table:
+    type: File
+    format: iana:application/x-r-data
+    doc: A rdata file containing one xsAnnotate object 
+    outputBinding:
+      glob: ouput.Rdata
+  peak_plot:
+    type: File
+    format: iana:application/pdf
+    doc: The plotted pseudo spectra with their adduct annotations
+    outputBinding:
+      glob: ouput.pdf
+
+baseCommand: findAdducts.r
+
+arguments:
+ - input=$(inputs.xs_annotate.path)
+ - output=output.Rdata
+ - ppm=$(inputs.ppm)
+ - polarity=$(inputs.polarity)
+ - output.pdf=output.pdf
+ - plotpdf=true
+ - rules=$(inputs.rules)
+
+doc: |
+  Perform precursor adduct annotation using CAMERA. 
+
+  Annotate adducts (and fragments) for a xsAnnotate object. Returns a
+  xsAnnotate object with annotated pseudospectra. It is recommended to use
+  **camera-find-isotopes** beforehand.
+
+  **Please cite**: 
+  R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
+
+  **References**
+  Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
+  an integrated strategy for compound spectra extraction and annotation of
+  liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
+  pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g. 
+
+$namespaces: 
+  iana: "https://www.iana.org/assignments/media-types/"

tools/phenomenal/ms/camera/camera-find-isotopes.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: CAMERA Find Isotopes
+
+hints:
+  DockerRequirement:
+    dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
+  SoftwareRequirement:
+    packages:
+      camera:
+        specs:
+          - https://bio.tools/camera
+          - https://identifiers.org/rrid/RRID:SCR_002466
+
+inputs:
+  xs_annotate:
+    type: File
+    format: iana:application/x-r-data
+    label: xsAnnotate file
+    doc: A rdata file with a xsAnnotate object from one sample
+  max_charge:
+    type: int
+    label: Max. number of the isotope charge
+
+outputs:
+  annotated_isotopes:
+    type: File
+    format: iana:application/x-r-data
+    doc: A rdata file containing one xsAnnotate object 
+    outputBinding:
+      glob: ouput.Rdata
+
+baseCommand: findIsotopes.r
+
+arguments:
+ - input=$(inputs.xs_annotate.path)
+ - output=output.Rdata
+ - maxcharge=$(inputs.max_charge)
+
+doc: |
+  Annotate isotope peaks for a xsAnnotate object. Returns a xsAnnotate object
+  with annotated isotopes.
+
+  **Please cite**: 
+  R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
+
+  **References**
+  Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
+  an integrated strategy for compound spectra extraction and annotation of
+  liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
+  pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g. 
+
+$namespaces: 
+  iana: "https://www.iana.org/assignments/media-types/"
+

tools/phenomenal/ms/camera/camera-group-corr.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: CAMERA Group Corr
+
+hints:
+  DockerRequirement:
+    dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
+  SoftwareRequirement:
+    packages:
+      camera:
+        specs:
+          - https://bio.tools/camera
+          - https://identifiers.org/rrid/RRID:SCR_002466
+
+inputs:
+  xs_annotate:
+    type: File
+    format: iana:application/x-r-data
+    label: xsAnnotate file
+    doc: A rdata file with a xsAnnotate object from one sample
+  correlation:
+    type: float
+    label: The correlation threshold for EIC correlation
+  p_value:
+    type: float
+    label: The p-value threshold for testing correlation of significance
+
+outputs:
+  grouped_peaks:
+    type: File
+    format: iana:application/x-r-data
+    doc: |
+      a rData file containing one xsAnnotate object containing grouped peaks in
+      so called pseudospectra
+    outputBinding:
+      glob: ouput.Rdata
+
+baseCommand: groupCorr.r
+
+arguments:
+ - input=$(inputs.xs_annotate.path)
+ - output=output.Rdata
+ - correlations=$(inputs.correlation)
+ - pvalue=$(inputs.pvalue)
+
+doc: |
+  Peak grouping after correlation information into pseudospectrum
+  groups for an xsAnnotate object.  
+
+  **Please cite**: 
+  R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
+
+  **References**
+  Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
+  an integrated strategy for compound spectra extraction and annotation of
+  liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
+  pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g. 
+
+$namespaces: 
+  iana: "https://www.iana.org/assignments/media-types/"
+

tools/phenomenal/ms/camera/camera-group-fwhm.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: CAMERA Group FWHM
+
+hints:
+  DockerRequirement:
+    dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
+  SoftwareRequirement:
+    packages:
+      camera:
+        specs:
+          - https://bio.tools/camera
+          - https://identifiers.org/rrid/RRID:SCR_002466
+
+inputs:
+  xs_annotate:
+    type: File
+    format: iana:application/x-r-data
+    label: xsAnnotate file
+    doc: A rdata file with a xsAnnotate object from one sample
+  sigma:
+    type: float
+    label: The multiplier of the standard deviation
+  per_fwhm:
+    type: float
+    label: Percentage of the width of the FWHM
+  intensity_values:
+    type: string
+    label: Intensity values for ordering.
+    doc: Allowed values are into, maxo, intb
+
+outputs:
+  grouped_peaks:
+    type: File
+    format: iana:application/x-r-data
+    doc: |
+      a rData file containing one xsAnnotate object containing grouped peaks in
+      so called pseudospectra
+    outputBinding:
+      glob: ouput.Rdata
+
+baseCommand: groupFWHM.r
+
+arguments:
+ - input=$(inputs.xs_annotate.path)
+ - output=output.Rdata
+ - sigma=$(inputs.sigma)
+ - perfwhm=$(inputs.per_fwhm)
+ - intval=$(inputs.intensity_values)
+
+doc: |
+  Group peaks of a xsAnnotate object according to their retention time into
+  pseudospectra-groups. Uses the peak FWHMs as grouping borders.
+
+  **Please cite**: 
+  R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
+
+  **References**
+  Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
+  an integrated strategy for compound spectra extraction and annotation of
+  liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
+  pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g. 
+
+$namespaces: 
+  iana: "https://www.iana.org/assignments/media-types/"
+