doc: Specify command inputs in a separate argument.

* doc/capture-output-file-with-parameter-reference.scm,
doc/capture-output-file.scm, doc/capture-stdout.scm, doc/checksum.scm,
doc/decompress-compile-run.scm, doc/hello-world.scm: Specify command
inputs in a separate argument.
* doc/ccwl.skb (Tutorial)[First example]: Update description of
command definition accordingly.

7 files changed, 45 insertions, 32 deletions

diff --git a/doc/capture-output-file-with-parameter-reference.scm b/doc/capture-output-file-with-parameter-reference.scm
index 3104fae..bb5476b 100644
--- a/doc/capture-output-file-with-parameter-reference.scm
+++ b/doc/capture-output-file-with-parameter-reference.scm
@@ -1,9 +1,9 @@
 (define extract-specific-file
-  (command #:run "tar" "--extract" "--file" (input 'archive #:type 'File)
-                                            (input 'extractfile #:type 'string)
-           #:outputs (output 'extracted-file
-                             #:type 'File
-                             #:binding '((glob . "$(inputs.extractfile)")))))
+  (command #:inputs (archive #:type 'File) (extractfile #:type 'string)
+           #:run "tar" "--extract" "--file" archive extractfile
+           #:outputs (extracted-file
+                      #:type 'File
+                      #:binding '((glob . "$(inputs.extractfile)")))))
 
 (workflow ((archive #:type File) (extractfile #:type string))
   (extract-specific-file #:archive archive #:extractfile extractfile))
diff --git a/doc/capture-output-file.scm b/doc/capture-output-file.scm
index b13549e..6c5dbbd 100644
--- a/doc/capture-output-file.scm
+++ b/doc/capture-output-file.scm
@@ -1,8 +1,9 @@
 (define extract
-  (command #:run "tar" "--extract" "--file" (input 'archive #:type 'File)
-           #:outputs (output 'extracted-file
-                             #:type 'File
-                             #:binding '((glob . "hello.txt")))))
+  (command #:inputs (archive #:type 'File)
+           #:run "tar" "--extract" "--file" archive
+           #:outputs (extracted-file
+                      #:type 'File
+                      #:binding '((glob . "hello.txt")))))
 
 (workflow ((archive #:type File))
   (extract #:archive archive))
diff --git a/doc/capture-stdout.scm b/doc/capture-stdout.scm
index 1f26a95..6913809 100644
--- a/doc/capture-stdout.scm
+++ b/doc/capture-stdout.scm
@@ -1,6 +1,7 @@
 (define print
-  (command #:run "echo" (input 'message #:type 'string)
-           #:outputs (output 'printed-message #:type 'stdout)))
+  (command #:inputs (message #:type 'string)
+           #:run "echo" message
+           #:outputs (printed-message #:type 'stdout)))
 
 (workflow ((message #:type string))
   (print #:message message))
diff --git a/doc/ccwl.skb b/doc/ccwl.skb
index 57baa94..f31cba8 100644
--- a/doc/ccwl.skb
+++ b/doc/ccwl.skb
@@ -58,12 +58,16 @@ string.])
 
       (p [The first form in this code defines the ,(code "print")
 command. This form is the equivalent of defining a
-,(code "CommandLineTool") class workflow in CWL. All arguments after
-,(code "#:run") specify the command that will be run. One of those
-arguments ,(code "(input 'message #:type 'string)") refers to a
-,(code "string") type input named ,(code "message"). Notice how the
-command definition is very close to a shell command, only that it is
-slightly annotated with inputs and their types.])
+,(code "CommandLineTool") class workflow in CWL. The arguments after
+,(code "#:inputs") define the inputs to the workflow. The arguments
+after ,(code "#:run") specify the command that will be run. The input
+,(code "(message #:type 'string)") defines a ,(code "string") type
+input named ,(code "message"). The command defined in the
+,(code "#:run") argument is the command itself followed by a list of
+command arguments. One of the arguments references the input
+,(code "message"). Notice how the command definition is very close to
+a shell command, only that it is slightly annotated with inputs and
+their types.])
 
       (p [The second form describes the actual workflow and is the
 equivalent of defining a ,(code "Workflow") class workflow in CWL. The
diff --git a/doc/checksum.scm b/doc/checksum.scm
index 206c2a0..4d8bfaf 100644
--- a/doc/checksum.scm
+++ b/doc/checksum.scm
@@ -1,14 +1,17 @@
 (define md5sum
-  (command #:run "md5sum" (input 'file #:type 'File)
-           #:outputs (output 'md5 #:type 'stdout)))
+  (command #:inputs (file #:type 'File)
+           #:run "md5sum" file
+           #:outputs (md5 #:type 'stdout)))
 
 (define sha1sum
-  (command #:run "sha1sum" (input 'file #:type 'File)
-           #:outputs (output 'sha1 #:type 'stdout)))
+  (command #:inputs (file #:type 'File)
+           #:run "sha1sum" file
+           #:outputs (sha1 #:type 'stdout)))
 
 (define sha256sum
-  (command #:run "sha256sum" (input 'file #:type 'File)
-           #:outputs (output 'sha256 #:type 'stdout)))
+  (command #:inputs (file #:type 'File)
+           #:run "sha256sum" file
+           #:outputs (sha256 #:type 'stdout)))
 
 (workflow ((file #:type File))
   (tee (md5sum #:file file)
diff --git a/doc/decompress-compile-run.scm b/doc/decompress-compile-run.scm
index 437fb41..a2c58bb 100644
--- a/doc/decompress-compile-run.scm
+++ b/doc/decompress-compile-run.scm
@@ -1,16 +1,19 @@
 (define decompress
-  (command #:run "gzip" "--stdout" "--decompress" (input 'compressed #:type 'File)
-           #:outputs (output 'decompressed #:type 'stdout)))
+  (command #:inputs (compressed #:type 'File)
+           #:run "gzip" "--stdout" "--decompress" compressed
+           #:outputs (decompressed #:type 'stdout)))
 
 (define compile
-  (command #:run "gcc" "-x" "c" (input 'source #:type 'File)
-           #:outputs (output 'executable
-                             #:type 'File
-                             #:binding '((glob . "a.out")))))
+  (command #:inputs (source #:type 'File)
+           #:run "gcc" "-x" "c" source
+           #:outputs (executable
+                      #:type 'File
+                      #:binding '((glob . "a.out")))))
 
 (define run
-  (command #:run (input 'executable)
-           #:outputs (output 'stdout #:type 'stdout)))
+  (command #:inputs executable
+           #:run executable
+           #:outputs (stdout #:type 'stdout)))
 
 (workflow ((compressed-source #:type File))
   (pipe (decompress #:compressed compressed-source)
diff --git a/doc/hello-world.scm b/doc/hello-world.scm
index 262b99f..1624053 100644
--- a/doc/hello-world.scm
+++ b/doc/hello-world.scm
@@ -1,5 +1,6 @@
 (define print
-  (command #:run "echo" (input 'message #:type 'string)))
+  (command #:inputs (message #:type 'string)
+           #:run "echo" message))
 
 (workflow ((message #:type string))
   (print #:message message))