# HG changeset patch
# User hackdna
# Date 1368484057 14400
# Node ID ca9a5aa3a59a38daba205d88eacd99338378d97f
# Parent  b72564825e0c4c8b52c2d1ee461ba521658ee052
Update sample workflows to provide empty output file option.

diff -r b72564825e0c -r ca9a5aa3a59a Test_workflow__SPP_analog.ga
--- a/Test_workflow__SPP_analog.ga	Mon May 13 18:27:14 2013 -0400
+++ b/Test_workflow__SPP_analog.ga	Mon May 13 18:27:37 2013 -0400
@@ -74,7 +74,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -103,7 +103,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -132,7 +132,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -161,7 +161,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -190,7 +190,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -219,7 +219,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -248,7 +248,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -301,7 +301,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_2-6/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"sleep_time\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"input_file1\": \"null\", \"input_file2\": \"null\"}", 
+            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"sleep_time\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"input_file1\": \"null\", \"input_file2\": \"null\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -330,7 +330,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -359,7 +359,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -388,7 +388,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -417,7 +417,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -446,7 +446,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -475,7 +475,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
@@ -504,7 +504,7 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/hackdna/refinery_test/refinery_test_1-1/0.1", 
-            "tool_state": "{\"__page__\": 0, \"stdout\": \"\\\"False\\\"\", \"input_file\": \"null\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
+            "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"stdout\": \"\\\"False\\\"\", \"exit_code\": \"\\\"0\\\"\", \"p_fail\": \"\\\"0.0\\\"\", \"empty_outfile\": \"\\\"False\\\"\", \"stderr\": \"\\\"False\\\"\", \"sleep_time\": \"\\\"0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []