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mr-cmr-c
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use working container
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‎tools/phenomenal/ms/camera/camera-annotate-peaks.cwl

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ label: CAMERA Annotate Peaks
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hints:
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DockerRequirement:
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dockerPull: quay.io/biocontainers/bioconductor-camera
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dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
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SoftwareRequirement:
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packages:
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camera:
@@ -32,7 +32,7 @@ outputs:
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baseCommand: xsAnnotate.r
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arguments:
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- input=$(inputs.camera_annotate_peaks.path
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- input=$(inputs.camera_annotate_peaks.path)
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- output=output.Rdata
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doc: |

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

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ label: CAMERA Find Adducts
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hints:
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DockerRequirement:
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dockerPull: quay.io/biocontainers/bioconductor-camera
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dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
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SoftwareRequirement:
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packages:
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camera:

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

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Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@ label: CAMERA Find Isotopes
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hints:
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DockerRequirement:
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dockerPull: quay.io/biocontainers/bioconductor-camera
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dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
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SoftwareRequirement:
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packages:
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camera:

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

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@@ -0,0 +1,63 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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class: CommandLineTool
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label: CAMERA Group Corr
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hints:
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DockerRequirement:
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dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
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SoftwareRequirement:
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packages:
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camera:
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specs:
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- https://bio.tools/camera
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- https://identifiers.org/rrid/RRID:SCR_002466
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inputs:
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xs_annotate:
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type: File
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format: iana:application/x-r-data
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label: xsAnnotate file
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doc: A rdata file with a xsAnnotate object from one sample
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correlation:
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type: float
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label: The correlation threshold for EIC correlation
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p_value:
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type: float
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label: The p-value threshold for testing correlation of significance
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outputs:
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grouped_peaks:
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type: File
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format: iana:application/x-r-data
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doc: |
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a rData file containing one xsAnnotate object containing grouped peaks in
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so called pseudospectra
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outputBinding:
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glob: ouput.Rdata
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baseCommand: groupCorr.r
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arguments:
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- input=$(inputs.xs_annotate.path)
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- output=output.Rdata
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- correlations=$(inputs.correlation)
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- pvalue=$(inputs.pvalue)
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doc: |
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Peak grouping after correlation information into pseudospectrum
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groups for an xsAnnotate object.
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**Please cite**:
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R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
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**References**
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Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
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an integrated strategy for compound spectra extraction and annotation of
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liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
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pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g.
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$namespaces:
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iana: "https://www.iana.org/assignments/media-types/"
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‎tools/phenomenal/ms/camera/camera-group-fwhm.cwl

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@@ -0,0 +1,68 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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class: CommandLineTool
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label: CAMERA Group FWHM
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hints:
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DockerRequirement:
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dockerPull: container-registry.phenomenal-h2020.eu/phnmnl/camera
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SoftwareRequirement:
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packages:
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camera:
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specs:
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- https://bio.tools/camera
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- https://identifiers.org/rrid/RRID:SCR_002466
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inputs:
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xs_annotate:
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type: File
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format: iana:application/x-r-data
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label: xsAnnotate file
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doc: A rdata file with a xsAnnotate object from one sample
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sigma:
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type: float
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label: The multiplier of the standard deviation
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per_fwhm:
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type: float
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label: Percentage of the width of the FWHM
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intensity_values:
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type: string
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label: Intensity values for ordering.
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doc: Allowed values are into, maxo, intb
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outputs:
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grouped_peaks:
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type: File
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format: iana:application/x-r-data
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doc: |
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a rData file containing one xsAnnotate object containing grouped peaks in
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so called pseudospectra
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outputBinding:
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glob: ouput.Rdata
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baseCommand: groupFWHM.r
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arguments:
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- input=$(inputs.xs_annotate.path)
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- output=output.Rdata
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- sigma=$(inputs.sigma)
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- perfwhm=$(inputs.per_fwhm)
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- intval=$(inputs.intensity_values)
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doc: |
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Group peaks of a xsAnnotate object according to their retention time into
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pseudospectra-groups. Uses the peak FWHMs as grouping borders.
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**Please cite**:
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R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
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**References**
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Kuhl C, Tautenhahn R, Boettcher C, Larson TR and Neumann S (2012). "CAMERA:
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an integrated strategy for compound spectra extraction and annotation of
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liquid chromatography/mass spectrometry data sets." Analytical Chemistry, 84,
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pp. 283-289. http://pubs.acs.org/doi/abs/10.1021/ac202450g.
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$namespaces:
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iana: "https://www.iana.org/assignments/media-types/"
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‎tools/phenomenal/ms/xcms/xcms-blankfilter.cwl

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@@ -10,7 +10,7 @@ hints:
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- https://identifiers.org/rrid/RRID:SCR_015538
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- https://bio.tools/xcms
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DockerRequirement:
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dockerPull: biocontainers/xcms
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dockerPull: payamemami/xcms-container
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label: Filters out the peaks that have higher intensities in blank samples compared to selected samples.
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‎tools/phenomenal/ms/xcms/xcms-collect-peaks.cwl

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@@ -10,7 +10,7 @@ hints:
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- https://identifiers.org/rrid/RRID:SCR_015538
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- https://bio.tools/xcms
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DockerRequirement:
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dockerPull: biocontainers/xcms
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dockerPull: payamemami/xcms-container
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label: Combine XCMS-Set objects
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‎tools/phenomenal/ms/xcms/xcms-correct-rt.cwl

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- https://identifiers.org/rrid/RRID:SCR_015538
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- https://bio.tools/xcms
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DockerRequirement:
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dockerPull: biocontainers/xcms
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dockerPull: payamemami/xcms-container
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label: Correct differences between retention times between different samples using the `retcor` generic method.
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‎tools/phenomenal/ms/xcms/xcms-dilutionfilter.cwl

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@@ -10,7 +10,7 @@ hints:
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- https://identifiers.org/rrid/RRID:SCR_015538
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- https://bio.tools/xcms
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DockerRequirement:
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dockerPull: biocontainers/xcms
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dockerPull: payamemami/xcms-container
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label: Dilution Filter
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doc: |

‎tools/phenomenal/ms/xcms/xcms-fill-peaks.cwl

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@@ -10,7 +10,7 @@ hints:
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- https://identifiers.org/rrid/RRID:SCR_015538
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- https://bio.tools/xcms
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DockerRequirement:
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dockerPull: biocontainers/xcms
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dockerPull: payamemami/xcms-container
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label: XCMS Fill Peaks
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doc: |

‎tools/phenomenal/ms/xcms/xcms-find-peaks.cwl

+3-4
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@@ -2,8 +2,6 @@
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: findPeaks.r
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hints:
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SoftwareRequirement:
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packages:
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- https://identifiers.org/rrid/RRID:SCR_015538
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- https://bio.tools/xcms
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DockerRequirement:
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dockerPull: biocontainers/xcms
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dockerPull: payamemami/xcms-container
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inputs:
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spectra:
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glob: output.Rdata
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doc: A rdata file containing a XCMS-Set generated from the input mzML file
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baseCommand: findPeaks.r
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arguments:
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- output=output.Rdata
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- ppm=$(inputs.ppm)
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label: XMCS Find Peaks
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$namespaces:
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iana: "https://www.iana.org/assignments/media-types/"
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edam: "http://edamontology.org"

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