code review

LICENSE.txt

@@ -0,0 +1,27 @@
+Copyright (c) 2015, Broad Institute, Inc.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name Broad Institute, Inc. nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE

README.md

@@ -38,7 +38,7 @@ java -jar cromwell.jar <action> <parameters>
 Actions:
 parse <WDL file>
 
-  Compares a WDL file against the grammar and prints out an
+  Compares a WDL file against the grammar and writes out an
   abstract syntax tree if it is valid, and a syntax error
   otherwise.  Note that higher-level AST checks are not done
   via this sub-command and the 'validate' subcommand should
@@ -65,12 +65,12 @@ highlight <WDL file> <html|console>
 
 ## validate
 
-Given a WDL file, this runs the full syntax checker over the file and resolves imports in the process.  If any syntax errors are found, they are printed out.  Otherwise the program exits.
+Given a WDL file, this runs the full syntax checker over the file and resolves imports in the process.  If any syntax errors are found, they are written out.  Otherwise the program exits.
 
 Error if a `call` references a task that doesn't exist:
 
 ```
-$ java -jar cromwell.jar validate 2.wdl
+$ java -jar wdltool.jar validate 2.wdl
 ERROR: Call references a task (BADps) that doesn't exist (line 22, col 8)
 
   call BADps
@@ -81,7 +81,7 @@ ERROR: Call references a task (BADps) that doesn't exist (line 22, col 8)
 Error if namespace and task have the same name:
 
 ```
-$ java -jar cromwell.jar validate 5.wdl
+$ java -jar wdltool.jar validate 5.wdl
 ERROR: Task and namespace have the same name:
 
 Task defined here (line 3, col 6):
@@ -100,7 +100,7 @@ import "ps.wdl" as ps
 Examine a WDL file with one workflow in it, compute all the inputs needed for that workflow and output a JSON template that the user can fill in with values.  The keys in this document should remain unchanged.  The values tell you what type the parameter is expecting.  For example, if the value were `Array[String]`, then it's expecting a JSON array of JSON strings, like this: `["string1", "string2", "string3"]`
 
 ```
-$ java -jar cromwell.jar inputs 3step.wdl
+$ java -jar wdltool.jar inputs 3step.wdl
 {
   "three_step.cgrep.pattern": "String"
 }
@@ -110,10 +110,10 @@ This inputs document is used as input to the `run` subcommand.
 
 ## parse
 
-Given a WDL file input, this does grammar level syntax checks and prints out the resulting abstract syntax tree.
+Given a WDL file input, this does grammar level syntax checks and writes out the resulting abstract syntax tree.
 
 ```
-$ echo "workflow wf {}" | java -jar cromwell.jar parse /dev/stdin
+$ echo "workflow wf {}" | java -jar wdltool.jar parse /dev/stdin
 (Document:
   imports=[],
   definitions=[
@@ -149,7 +149,7 @@ workflow wf {
 This WDL file can be formatted in HTML as follows:
 
 ```
-$ java -jar cromwell.jar highlight test.wdl html
+$ java -jar wdltool.jar highlight test.wdl html
 <span class="keyword">task</span> <span class="name">abc</span> {
   <span class="type">String</span> <span class="variable">in</span>
   <span class="section">command</span> {