generate-red-and-job.py

Author: Christoph Jansen

generate-red-and-job.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+
+from ruamel.yaml import YAML
+
+yaml = YAML(typ='safe')
+
+
+INPUT_DIR_LISTING = [{
+    'class': 'Directory',
+    'basename': 'datasets',
+    'listing': [{
+        'class': 'File',
+        'basename': 'lfq_spikein_dilution_1.mzML'
+    }, {
+        'class': 'File',
+        'basename': 'lfq_spikein_dilution_2.mzML'
+    }, {
+        'class': 'File',
+        'basename': 'lfq_spikein_dilution_3.mzML'
+    }]
+}, {
+    'class': 'Directory',
+    'basename': 'databases',
+    'listing': [{
+        'class': 'File',
+        'basename': 's_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta'
+    }, {
+        'class': 'File',
+        'basename': 's_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.phr'
+    }, {
+        'class': 'File',
+        'basename': 's_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.pin'
+    }, {
+        'class': 'File',
+        'basename': 's_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.psq'
+    }, {
+        'class': 'File',
+        'basename': 'uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta'
+    }, {
+        'class': 'File',
+        'basename': 'uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.phr'
+    }, {
+        'class': 'File',
+        'basename': 'uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.pin'
+    }, {
+        'class': 'File',
+        'basename': 'uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.psq'
+    }]
+}]
+
+DATABASE_NAME = 's_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta'
+
+
+with open('knime-labelfree-quantification.cwl.yml') as f:
+    cwl = yaml.load(f)
+
+docker_image_url = cwl['requirements']['DockerRequirement']['dockerPull']
+
+del cwl['requirements']
+
+
+red = {
+    'redVersion': '7',
+    'cli': cwl,
+    'inputs': {
+        'input_dir': {
+            'class': 'Directory',
+            'connector': {
+                'command': 'red-connector-http-archive',
+                'access': {
+                    'url': 'https://s3.denbi.uni-tuebingen.de/fb-test/demo_container/cibi_user_meeting_2018/labelfree_example.tar.gz',
+                    'archiveFormat': 'gztar'
+                }
+            },
+            'listing': INPUT_DIR_LISTING
+        },
+        'database_name': DATABASE_NAME
+    },
+    'container': {
+        'engine': 'docker',
+        'settings': {
+            'image': {
+                'url': docker_image_url
+            }
+        }
+    }
+}
+
+job = {
+    'input_dir': {
+        'class': 'Directory',
+        'location': 'labelfree_example',
+        'listing': INPUT_DIR_LISTING
+    },
+    'database_name': DATABASE_NAME
+}
+
+with open('knime-labelfree-quantification.red.yml', 'w') as f:
+    yaml.dump(red, f)
+
+with open('job.yml', 'w') as f:
+    yaml.dump(job, f)
+

generate-red.py

@@ -1,4 +1,28 @@
+database_name: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta
 input_dir:
-  class: "Directory"
-  location: "labelfree_example"
-database_name: "s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta"
+  class: Directory
+  listing:
+  - basename: datasets
+    class: Directory
+    listing:
+    - {basename: lfq_spikein_dilution_1.mzML, class: File}
+    - {basename: lfq_spikein_dilution_2.mzML, class: File}
+    - {basename: lfq_spikein_dilution_3.mzML, class: File}
+  - basename: databases
+    class: Directory
+    listing:
+    - {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta, class: File}
+    - {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.phr,
+      class: File}
+    - {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.pin,
+      class: File}
+    - {basename: s_pyo_sf370_potato_human_target_decoy_with_contaminants.fasta.psq,
+      class: File}
+    - {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta, class: File}
+    - {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.phr,
+      class: File}
+    - {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.pin,
+      class: File}
+    - {basename: uniprot-s-pyogenes-sf370-plus-potato-and-human-spike-ins.fasta.psq,
+      class: File}
+  location: labelfree_example