# HG changeset patch
# User iuc
# Date 1444928890 14400
# Node ID 3d44a3855011aec6c3c0b8ffdb7805010a9865d5
# Parent f9305f8811b8e55038802549f5d2aba6849f2e16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
diff -r f9305f8811b8 -r 3d44a3855011 test.xml
--- a/test.xml Thu Oct 15 13:05:45 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-test:1-17\n-AACTGATCGATCGATCG\n->test:29-33\n-ACATG\n+#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts\n+test\t33\t7\t5\t5\t5\t0\t0\t11\t6\t0\t0\t0\n\n-------------------- >> begin captured logging << --------------------\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions.upload_common: INFO: tool upload1 created job id 3\ngalaxy.tools.execute: DEBUG: Tool [upload1] created job [3] (698.515 ms)\nrequests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/tmpCMllB5/job_working_directory/000/3\ngalaxy.jobs.handler: DEBUG: (3) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local)\ngalaxy.jobs.runners: DEBUG: Job [3] queued (1343.475 ms)\ngalaxy.jobs.handler: INFO: (3) Job dispatched\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \'samtools\'\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \'samtools\', ignoring\ngalaxy.jobs.runners: DEBUG: (3) command is: python /home/hxr/work/galaxy/tools/data_source/upload.py /home/hxr/work/galaxy /tmp/tmpCMllB5/tmp/tmpIw2yGA /tmp/tmpCMllB5/tmp/tmp6bjnD8 3:/tmp/tmpCMllB5/job_working_directory/000/3/dataset_3_files:/tmp/tmpCMllB5/files/000/dataset_3.dat; return_code=$?; python "/tmp/tmpCMllB5/job_working_directory/000/3/set_metadata_l3EI2j.py" "/tmp/tmpCMllB5/tmp/tmpIw2yGA" "/tmp/tmpCMllB5/job_working_directory/000/3/galaxy.json" "/tmp/tmpCMllB5/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_dPLYGW,/tmp/tmpCMllB5/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_cdS4Q9,/tmp/tmpCMllB5/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_PriNuI,/tmp/tmpCMllB5/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_2hfSyu,/tmp/tmpCMllB5/files/000/dataset_3.dat,/tmp/tmpCMllB5/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_7pu_Wo" 5242880; sh -c "exit $return_code"\ngalaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/tmpCMllB5/job_working_directory/000/3/galaxy_3.sh\ngalaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local)\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpCMllB5/job_working_directory/000/3/galaxy_3.sh\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 3\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 3 ended (finish() executed in (1640.542 ms))\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.tools.actions: INFO: Handled output (441.631 ms)\ngalaxy.tools.actions: INFO: Verified access to datasets (9.077 ms)\ngalaxy.tools.execute: DEBUG: Tool [seqtk_comp] created job [4] (957.828 ms)\nrequests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (4) Working directory for job is: /tmp/tmpCMllB5/job_working_directory/000/4\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\ngalaxy.jobs.handler: DEBUG: (4) Dispatching to local runner\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local)\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners: DEBUG: Job [4] queued (268.598 ms)\ngalaxy.jobs.handler: INFO: (4) Job dispatched\ngalaxy.tools.deps: DEBUG: Building dependency shell command for dependency \'seqtk\'\ngalaxy.tools.deps: WARNING: Failed to resolve dependency on \'seqtk\', ignoring\ngalaxy.jobs.runners: DEBUG: (4) command is: seqtk comp /tmp/tmpCMllB5/files/000/dataset_3.dat | awk \'BEGIN{print "#chr\\tlength\\t#A\\t#C\\t#G\\t#T\\t#2\\t#3\\t#4\\t#CpG\\t#tv\\t#ts\\t#CpG-ts"}1\' > /tmp/tmpCMllB5/files/000/dataset_4.dat; return_code=$?; python "/tmp/tmpCMllB5/job_working_directory/000/4/set_metadata_OS_L8J.py" "/tmp/tmpCMllB5/tmp/tmpIw2yGA" "/tmp/tmpCMllB5/job_working_directory/000/4/galaxy.json" "/tmp/tmpCMllB5/job_working_directory/000/4/metadata_in_HistoryDatasetAssociation_4_IpnblQ,/tmp/tmpCMllB5/job_working_directory/000/4/metadata_kwds_HistoryDatasetAssociation_4_3bnNZN,/tmp/tmpCMllB5/job_working_directory/000/4/metadata_out_HistoryDatasetAssociation_4_sBHfWI,/tmp/tmpCMllB5/job_working_directory/000/4/metadata_results_HistoryDatasetAssociation_4_yuQ2fB,/tmp/tmpCMllB5/files/000/dataset_4.dat,/tmp/tmpCMllB5/job_working_directory/000/4/metadata_override_HistoryDatasetAssociation_4_ZCVTqC" 5242880; sh -c "exit $return_code"\ngalaxy.jobs.runners.local: DEBUG: (4) executing job script: /tmp/tmpCMllB5/job_working_directory/000/4/galaxy_4.sh\ngalaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local)\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpCMllB5/job_working_directory/000/4/galaxy_4.sh\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 4\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: job 4 ended (finish() executed in (638.998 ms))\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?full=true&key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff/display?raw=true&key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmpCMllB5/jobfiles, ofn: /tmp/tmpCMllB5/jobfiles/seqtk_cutn.out\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpCMllB5/jobfiles. saved /tmp/tmpCMllB5/jobfiles/seqtk_cutn.out\nbase.twilltestcase: INFO: ## files diff on /home/hxr/work/tools-iuc/tools/seqtk/test-data/seqtk_cutn.out and /tmp/tmpCMllB5/tmp/tmpJSB4jxseqtk_cutn.out lines_diff=0, found diff = 6\n--------------------- >> end captured logging << ---------------------']]>> begin tool stdout << -----------------------
-
------------------------ >> end tool stdout << ------------------------
-
----------------------- >> begin tool stderr << -----------------------
-
------------------------ >> end tool stderr << ------------------------
-
-]]>
\ No newline at end of file
diff -r f9305f8811b8 -r 3d44a3855011 tmp.html
--- a/tmp.html Thu Oct 15 13:05:45 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-
-
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-
-
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-
-Executive Summary
-
-
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-
-
-
-| Total |
-2 |
-
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-| Passed |
-1 |
-
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-| Error |
-0 |
-
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-| Failure |
-0 |
-
-
-| Skipped |
-0 |
-
-
-
-Detailed Results
-
-Job Passed
-
-Job Error! (State: failure)
-Command Line:
-seqtk comp /tmp/tmpiQOEjP/files/000/dataset_3.dat | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' > /tmp/tmpiQOEjP/files/000/dataset_4.dat
-exited with code 0.
-Test Output
-[u'History item different than expected, difference (using diff):\n( /home/hxr/work/tools-iuc/tools/seqtk/test-data/seqtk_cutn.out v. /tmp/tmpiQOEjP/tmp/tmpFeDB5Tseqtk_cutn.out )\n--- local_file\n+++ history_data\n@@ -1,4 +1,2 @@\n->test:1-17\n-AACTGATCGATCGATCG\n->test:29-33\n-ACATG\n+#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts\n+test\t33\t7\t5\t5\t5\t0\t0\t11\t6\t0\t0\t0\n']
-
-
diff -r f9305f8811b8 -r 3d44a3855011 tool_dependencies.xml
--- a/tool_dependencies.xml Thu Oct 15 13:05:45 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
-
-
-
diff -r f9305f8811b8 -r 3d44a3855011 tool_test_output.md
--- a/tool_test_output.md Thu Oct 15 13:05:45 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-# Tool Test Results (powered by Planemo)
-
-## Executive Summary
-
-| Test State | Count |
-| ---------- | ----- |
-| Total | 2 |
-| Passed | 1 |
-| Error | 0 |
-| Failure | 0 |
-| Skipped | 0 |
-
-
-## Detailed Results
-
-### functional.test_toolbox.TestForTool_seqtk_comp.test_tool_000000
-
-Job Passed
-
-
-### functional.test_toolbox.TestForTool_seqtk_comp.test_tool_000001
-
-Job Error! (State: failure)
-
-Command Line:
-
-```console
-seqtk comp /tmp/tmpe3FMDm/files/000/dataset_3.dat | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' > /tmp/tmpe3FMDm/files/000/dataset_4.dat
-```
-
-exited with code 0.
-
-#### Problems
-
-
-```console
-History item different than expected, difference (using diff):
-( /home/hxr/work/tools-iuc/tools/seqtk/test-data/seqtk_cutn.out v. /tmp/tmpe3FMDm/tmp/tmpguZsVkseqtk_cutn.out )
---- local_file
-+++ history_data
-@@ -1,4 +1,2 @@
-->test:1-17
--AACTGATCGATCGATCG
-->test:29-33
--ACATG
-+#chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
-+test 33 7 5 5 5 0 0 11 6 0 0 0
-
-```
-
-
-
-
-
diff -r f9305f8811b8 -r 3d44a3855011 tool_test_output.txt
--- a/tool_test_output.txt Thu Oct 15 13:05:45 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-There were problems with 1 out of 2 test(s) executed.
-
-seqtk_comp.test_tool_000000: success
-seqtk_comp.test_tool_000001: failure
- History item different than expected, difference (using diff):
- ( /home/hxr/work/tools-iuc/tools/seqtk/test-data/seqtk_cutn.out v. /tmp/tmpe3FMDm/tmp/tmpguZsVkseqtk_cutn.out )
- --- local_file
- +++ history_data
- @@ -1,4 +1,2 @@
- ->test:1-17
- -AACTGATCGATCGATCG
- ->test:29-33
- -ACATG
- +#chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
- +test 33 7 5 5 5 0 0 11 6 0 0 0
-