Merge branch 'master' into shell-commands

Peter Amstutz · Peter Amstutz · commit ccc71ff3be29 · 2015-10-12T10:28:48.000-04:00
Conflicts:
	draft-3/draft-3/revsort-job.json
	draft-3/draft-3/whale.txt
diff --git a/draft-3/draft-3/add-lines-wf.cwl b/draft-3/draft-3/add-lines-wf.cwl
@@ -1 +1 @@
-../draft-2/add-lines-wf.cwl
+../../draft-2/draft-2/add-lines-wf.cwl
diff --git a/draft-3/draft-3/binding-test.cwl b/draft-3/draft-3/binding-test.cwl
@@ -1 +1 @@
-../draft-2/binding-test.cwl
+../../draft-2/draft-2/binding-test.cwl
diff --git a/draft-3/draft-3/bwa-mem-job.json b/draft-3/draft-3/bwa-mem-job.json
@@ -1 +1 @@
-../draft-2/bwa-mem-job.json
+../../draft-2/draft-2/bwa-mem-job.json
diff --git a/draft-3/draft-3/cat-job.json b/draft-3/draft-3/cat-job.json
@@ -1 +1 @@
-../draft-2/cat-job.json
+../../draft-2/draft-2/cat-job.json
diff --git a/draft-3/draft-3/cat-n-job.json b/draft-3/draft-3/cat-n-job.json
@@ -1 +1 @@
-../draft-2/cat-n-job.json
+../../draft-2/draft-2/cat-n-job.json
diff --git a/draft-3/draft-3/cat1-tool.cwl b/draft-3/draft-3/cat1-tool.cwl
@@ -1 +1 @@
-../draft-2/cat1-tool.cwl
+../../draft-2/draft-2/cat1-tool.cwl
diff --git a/draft-3/draft-3/cat2-tool.cwl b/draft-3/draft-3/cat2-tool.cwl
@@ -1 +1 @@
-../draft-2/cat2-tool.cwl
+../../draft-2/draft-2/cat2-tool.cwl
diff --git a/draft-3/draft-3/cat3-tool.cwl b/draft-3/draft-3/cat3-tool.cwl
@@ -1 +1 @@
-../draft-2/cat3-tool.cwl
+../../draft-2/draft-2/cat3-tool.cwl
diff --git a/draft-3/draft-3/cat4-tool.cwl b/draft-3/draft-3/cat4-tool.cwl
@@ -1 +1 @@
-../draft-2/cat4-tool.cwl
+../../draft-2/draft-2/cat4-tool.cwl
diff --git a/draft-3/draft-3/cat5-tool.cwl b/draft-3/draft-3/cat5-tool.cwl
@@ -1 +1 @@
-../draft-2/cat5-tool.cwl
+../../draft-2/draft-2/cat5-tool.cwl
diff --git a/draft-3/draft-3/count-lines3-job.json b/draft-3/draft-3/count-lines3-job.json
@@ -1 +1 @@
-../draft-2/count-lines3-job.json
+../../draft-2/draft-2/count-lines3-job.json
diff --git a/draft-3/draft-3/count-lines4-job.json b/draft-3/draft-3/count-lines4-job.json
@@ -1 +1 @@
-../draft-2/count-lines4-job.json
+../../draft-2/draft-2/count-lines4-job.json
diff --git a/draft-3/draft-3/count-lines6-job.json b/draft-3/draft-3/count-lines6-job.json
@@ -1 +1 @@
-../draft-2/count-lines6-job.json
+../../draft-2/draft-2/count-lines6-job.json
diff --git a/draft-3/draft-3/echo-tool.cwl b/draft-3/draft-3/echo-tool.cwl
@@ -1 +1 @@
-../draft-2/echo-tool.cwl
+../../draft-2/draft-2/echo-tool.cwl
diff --git a/draft-3/draft-3/empty.json b/draft-3/draft-3/empty.json
@@ -1 +1 @@
-../draft-2/empty.json
+../../draft-2/draft-2/empty.json
diff --git a/draft-3/draft-3/env-job.json b/draft-3/draft-3/env-job.json
@@ -1 +1 @@
-../draft-2/env-job.json
+../../draft-2/draft-2/env-job.json
diff --git a/draft-3/draft-3/env-tool1.cwl b/draft-3/draft-3/env-tool1.cwl
@@ -1 +1 @@
-../draft-2/env-tool1.cwl
+../../draft-2/draft-2/env-tool1.cwl
diff --git a/draft-3/draft-3/env-tool2.cwl b/draft-3/draft-3/env-tool2.cwl
@@ -1 +1 @@
-../draft-2/env-tool2.cwl
+../../draft-2/draft-2/env-tool2.cwl
diff --git a/draft-3/draft-3/hello.txt b/draft-3/draft-3/hello.txt
@@ -1 +1 @@
-../draft-2/hello.txt
+../../draft-2/draft-2/hello.txt
diff --git a/draft-3/draft-3/index.py b/draft-3/draft-3/index.py
@@ -1 +1 @@
-../draft-2/index.py
+../../draft-2/draft-2/index.py
diff --git a/draft-3/draft-3/node-engine.cwl b/draft-3/draft-3/node-engine.cwl
@@ -1 +1 @@
-../draft-2/node-engine.cwl
+../../draft-2/draft-2/node-engine.cwl
diff --git a/draft-3/draft-3/number.txt b/draft-3/draft-3/number.txt
@@ -1 +1 @@
-../draft-2/number.txt
+../../draft-2/draft-2/number.txt
diff --git a/draft-3/draft-3/parseInt-job.json b/draft-3/draft-3/parseInt-job.json
@@ -1 +1 @@
-../draft-2/parseInt-job.json
+../../draft-2/draft-2/parseInt-job.json
diff --git a/draft-3/draft-3/rename-job.json b/draft-3/draft-3/rename-job.json
@@ -1 +1 @@
-../draft-2/rename-job.json
+../../draft-2/draft-2/rename-job.json
diff --git a/draft-3/draft-3/rename.cwl b/draft-3/draft-3/rename.cwl
@@ -1 +1 @@
-../draft-2/rename.cwl
+../../draft-2/draft-2/rename.cwl
diff --git a/draft-3/draft-3/revsort-job.json b/draft-3/draft-3/revsort-job.json
diff --git a/draft-3/draft-3/revsort-job.json b/draft-3/draft-3/revsort-job.json
@@ -0,0 +1 @@
+../../draft-2/draft-2/revsort-job.json
diff --git a/draft-3/draft-3/revtool.cwl b/draft-3/draft-3/revtool.cwl
@@ -1 +1 @@
-../draft-2/revtool.cwl
+../../draft-2/draft-2/revtool.cwl
diff --git a/draft-3/draft-3/scatter-job1.json b/draft-3/draft-3/scatter-job1.json
@@ -1 +1 @@
-../draft-2/scatter-job1.json
+../../draft-2/draft-2/scatter-job1.json
diff --git a/draft-3/draft-3/scatter-job2.json b/draft-3/draft-3/scatter-job2.json
@@ -1 +1 @@
-../draft-2/scatter-job2.json
+../../draft-2/draft-2/scatter-job2.json
diff --git a/draft-3/draft-3/scatter-wf1.cwl b/draft-3/draft-3/scatter-wf1.cwl
@@ -1 +1 @@
-../draft-2/scatter-wf1.cwl
+../../draft-2/draft-2/scatter-wf1.cwl
diff --git a/draft-3/draft-3/scatter-wf2.cwl b/draft-3/draft-3/scatter-wf2.cwl
@@ -1 +1 @@
-../draft-2/scatter-wf2.cwl
+../../draft-2/draft-2/scatter-wf2.cwl
diff --git a/draft-3/draft-3/search-job.json b/draft-3/draft-3/search-job.json
@@ -1 +1 @@
-../draft-2/search-job.json
+../../draft-2/draft-2/search-job.json
diff --git a/draft-3/draft-3/search.py b/draft-3/draft-3/search.py
@@ -1 +1 @@
-../draft-2/search.py
+../../draft-2/draft-2/search.py
diff --git a/draft-3/draft-3/sorttool.cwl b/draft-3/draft-3/sorttool.cwl
@@ -1 +1 @@
-../draft-2/sorttool.cwl
+../../draft-2/draft-2/sorttool.cwl
diff --git a/draft-3/draft-3/tmap-job.json b/draft-3/draft-3/tmap-job.json
@@ -1 +1 @@
-../draft-2/tmap-job.json
+../../draft-2/draft-2/tmap-job.json
diff --git a/draft-3/draft-3/underscore.js b/draft-3/draft-3/underscore.js
@@ -1 +1 @@
-../draft-2/underscore.js
+../../draft-2/draft-2/underscore.js
diff --git a/draft-3/draft-3/wc-job.json b/draft-3/draft-3/wc-job.json
@@ -1 +1 @@
-../draft-2/wc-job.json
+../../draft-2/draft-2/wc-job.json
diff --git a/draft-3/draft-3/wc-tool.cwl b/draft-3/draft-3/wc-tool.cwl
@@ -1 +1 @@
-../draft-2/wc-tool.cwl
+../../draft-2/draft-2/wc-tool.cwl
diff --git a/draft-3/draft-3/whale.txt b/draft-3/draft-3/whale.txt
diff --git a/draft-3/draft-3/whale.txt b/draft-3/draft-3/whale.txt
@@ -0,0 +1 @@
+../../draft-2/draft-2/whale.txt

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/add-lines-wf.cwl`
	`1`	`+../../draft-2/draft-2/add-lines-wf.cwl`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/binding-test.cwl`
	`1`	`+../../draft-2/draft-2/binding-test.cwl`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/bwa-mem-job.json`
	`1`	`+../../draft-2/draft-2/bwa-mem-job.json`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat-job.json`
	`1`	`+../../draft-2/draft-2/cat-job.json`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat-n-job.json`
	`1`	`+../../draft-2/draft-2/cat-n-job.json`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat1-tool.cwl`
	`1`	`+../../draft-2/draft-2/cat1-tool.cwl`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat2-tool.cwl`
	`1`	`+../../draft-2/draft-2/cat2-tool.cwl`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat3-tool.cwl`
	`1`	`+../../draft-2/draft-2/cat3-tool.cwl`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat4-tool.cwl`
	`1`	`+../../draft-2/draft-2/cat4-tool.cwl`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-../draft-2/cat5-tool.cwl`
	`1`	`+../../draft-2/draft-2/cat5-tool.cwl`