Add the Common Workflow Language standard (#3902)

* Add the language for the Common Workflow Language standards

* add CWL grammer

* add MIT licensed CWL sample

* script/set-language-ids --update for CWL

.gitmodules

@@ -883,3 +883,6 @@
 [submodule "vendor/grammars/atom-language-julia"]
 	path = vendor/grammars/atom-language-julia
 	url = https://github.com/JuliaEditorSupport/atom-language-julia
+[submodule "vendor/grammars/language-cwl"]
+	path = vendor/grammars/language-cwl
+	url = https://github.com/manabuishii/language-cwl

grammars.yml

@@ -387,6 +387,8 @@ vendor/grammars/language-csound:
 - source.csound-score
 vendor/grammars/language-css:
 - source.css
+vendor/grammars/language-cwl:
+- source.cwl
 vendor/grammars/language-emacs-lisp:
 - source.emacs.lisp
 vendor/grammars/language-fontforge:

lib/linguist/languages.yml

@@ -807,6 +807,19 @@ Common Lisp:
   codemirror_mode: commonlisp
   codemirror_mime_type: text/x-common-lisp
   language_id: 66
+Common Workflow Language:
+  alias: cwl
+  type: programming
+  ace_mode: yaml
+  codemirror_mode: yaml
+  codemirror_mime_type: text/x-yaml
+  extensions:
+  - ".cwl"
+  interpreters:
+  - cwl-runner
+  color: "#B5314C"
+  tm_scope: source.cwl
+  language_id: 988547172
 Component Pascal:
   type: programming
   color: "#B0CE4E"

samples/Common Workflow Language/trunk-peak-score.cwl

@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+# Originally from
+# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/utils/trunk-peak-score.cwl
+# Released under the MIT License:
+# https://github.com/Duke-GCB/GGR-cwl/blob/54e897263a702ff1074c8ac814b4bf7205d140dd/LICENSE
+# Converted to CWL v1.0 syntax using
+# https://github.com/common-workflow-language/cwl-upgrader
+# and polished by Michael R. Crusoe <mrc@commonwl.org>
+# All modifications also released under the MIT License
+cwlVersion: v1.0
+class: CommandLineTool
+doc: Trunk scores in ENCODE bed6+4 files
+
+hints:
+  DockerRequirement:
+    dockerPull: dukegcb/workflow-utils
+
+inputs:
+  peaks:
+    type: File
+  sep:
+    type: string
+    default: \t
+
+outputs:
+  trunked_scores_peaks:
+    type: stdout
+
+baseCommand: awk
+
+arguments:
+- -F $(inputs.sep)
+- BEGIN{OFS=FS}$5>1000{$5=1000}{print}
+- $(inputs.peaks.path)
+
+stdout: $(inputs.peaks.nameroot).trunked_scores$(inputs.peaks.nameext)

vendor/README.md

@@ -70,6 +70,7 @@ This is a list of grammars that Linguist selects to provide syntax highlighting
 - **ColdFusion CFC:** [SublimeText/ColdFusion](https://github.com/SublimeText/ColdFusion)
 - **COLLADA:** [textmate/xml.tmbundle](https://github.com/textmate/xml.tmbundle)
 - **Common Lisp:** [textmate/lisp.tmbundle](https://github.com/textmate/lisp.tmbundle)
+- **Common Workflow Language:** [manabuishii/language-cwl](https://github.com/manabuishii/language-cwl)
 - **Component Pascal:** [textmate/pascal.tmbundle](https://github.com/textmate/pascal.tmbundle)
 - **Cool:** [anunayk/cool-tmbundle](https://github.com/anunayk/cool-tmbundle)
 - **Coq:** [mkolosick/Sublime-Coq](https://github.com/mkolosick/Sublime-Coq)

vendor/licenses/grammar/language-cwl.txt

@@ -0,0 +1,26 @@
+---
+type: grammar
+name: language-cwl
+license: mit
+---
+MIT License
+
+Copyright (c) 2017 Manabu Ishii RIKEN Bioinformatics Research Unit
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.