metfrag and sirius CWL files from MAW (#146)

Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>

Author: zmahnoor14

metfrag/metfrag.cwl

@@ -0,0 +1,57 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+baseCommand: ['java', '-jar', '/usr/src/myapp/MetFragCommandLine-2.5.0.jar']
+
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/zmahnoor/maw-metfrag_2.5.0:1.0.4
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+    - entryname: param_file.txt
+      entry: |-
+        PeakListPath = $(inputs.PeakList.path)
+        IonizedPrecursorMass =  $(inputs.IonizedPrecursorMass)
+        PrecursorIonMode = $(inputs.PrecursorIonMode)
+        IsPositiveIonMode = $(inputs.IsPositiveIonMode)
+        MetFragDatabaseType = LocalCSV
+        LocalDatabasePath = $(inputs.LocalDatabase.path)
+        DatabaseSearchRelativeMassDeviation = 5
+        FragmentPeakMatchAbsoluteMassDeviation = 0.001
+        FragmentPeakMatchRelativeMassDeviation = 15
+        MetFragCandidateWriter = CSV
+        SampleName = $(inputs.SampleName)
+        ResultsPath = .
+        MetFragPreProcessingCandidateFilter = UnconnectedCompoundFilter
+        MetFragPostProcessingCandidateFilter = InChIKeyFilter
+        MaximumTreeDepth = 2
+        NumberThreads = $(runtime.cores)
+
+
+inputs: # additional inputs for all files; make them to show certain paths
+  PeakList: File
+  IonizedPrecursorMass: string
+  PrecursorIonMode: int
+  IsPositiveIonMode: boolean
+  LocalDatabase: File
+  SampleName: string
+  #MetFragDatabaseType: string
+  #DatabaseSearchRelativeMassDeviation: int
+  #FragmentPeakMatchAbsoluteMassDeviation: float
+  #FragmentPeakMatchRelativeMassDeviation: float
+  #MetFragCandidateWriter: string
+  #MetFragPreProcessingCandidateFilter: string
+  #MetFragPostProcessingCandidateFilter: string
+  #MaximumTreeDepth: int
+  #NumberThreads: int
+
+arguments:
+  - ParameterFile=param_file.txt
+
+outputs:
+  candidate_list:
+    type: File
+    outputBinding:
+        glob: "*.csv"

metfrag/metfrag_README.md

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+# How to use MetFrag in MAW:
+Pass the peaklist path, precursor mass, ion mode (1 for positive and 0 for negative), provide path to your local database, and a name for the result file
+```
+cwltool metfrag.cwl --PeakList path/to/peaklist.txt --IonizedPrecursorMass 123.45 --PrecursorIonMode 1 --IsPositiveIonMode True --LocalDatabase path/to/localdatabase.csv --SampleName result_file_name
+```

sirius/sirius.cwl

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+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+
+$namespaces:
+  cwltool: http://commonwl.org/cwltool#
+hints:
+  "cwltool:Secrets":
+    secrets:
+      - sirius_user
+      - sirius_password
+
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/zmahnoor/maw-sirius5:dev
+  InlineJavascriptRequirement: {}
+  ShellCommandRequirement: {}
+  EnvVarRequirement:
+    envDef:
+      SIRIUS_USER: $(inputs.sirius_user)
+      SIRIUS_PASSWORD: $(inputs.sirius_password)
+
+inputs:
+  sirius_user:
+    type: string
+  sirius_password:
+    type: string
+  spectrum:
+    type: File
+  profile:
+    type: string
+    default: "orbitrap"
+  candidates:
+    type: int
+    default: 30
+  ppm_max:
+    type: int
+    default: 5
+  ppm_max_ms2:
+    type: int
+    default: 15
+  database:
+    type: string
+    default: "coconut"
+  isotope:
+    type: boolean
+    default: False
+
+arguments:
+    - sirius
+    - login
+    - --user-env
+    - SIRIUS_USER
+    - --password-env
+    - SIRIUS_PASSWORD
+    - shellQuote: False
+      valueFrom: ";"
+    - sirius
+    - --input
+    - $(inputs.spectrum.path)
+    - --output
+    - $(inputs.spectrum.nameroot).json
+    - formula
+    - --profile
+    - $(inputs.profile)
+    - |
+      ${
+        if (inputs.isotope) {
+          return ["--no-isotope-filter",
+            "--no-isotope-score"];
+        } else {
+          return null;
+        }
+      }
+    - --candidates
+    - $(inputs.candidates)
+    - --ppm-max
+    - $(inputs.ppm_max)
+    - --ppm-max-ms2
+    - $(inputs.ppm_max_ms2)
+    - fingerprint
+    - structure
+    - --database
+    - $(inputs.database)
+    - compound-classes
+    - write-summaries
+    - --output
+    - $(inputs.spectrum.nameroot).json
+
+outputs:
+  results:
+    type: Directory
+    outputBinding:
+       glob: $(inputs.spectrum.nameroot).json

sirius/sirius_README.md

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+# How to use SIRIUS in MAW:
+Pass your SIRIUS user email and password and the ```.ms``` input file to the cwltool.
+```
+cwltool --enable-ext --cachedir cache --debug maw-sirius.cwl --sirius_user your_email --sirius_password your_password --spectrum /Users/mahnoorzulfiqar/Downloads/New_ms2_spectra_endo_pos/insilico/SIRIUS/no_isotope/1_NA_iso_NA_MS1p_446.230465650658_SIRIUS_param.ms
+```