Mercurial > repos > iuc > seqtk
changeset 10:3d44a3855011 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
| author | iuc |
|---|---|
| date | Thu, 15 Oct 2015 13:08:10 -0400 |
| parents | f9305f8811b8 |
| children | a13d872d7d8b |
| files | test.xml tmp.html tool_dependencies.xml tool_test_output.md tool_test_output.txt |
| diffstat | 5 files changed, 0 insertions(+), 145 deletions(-) [+] |
line wrap: on
line diff
--- 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 @@ -<?xml version="1.0" encoding="UTF-8"?><testsuite name="nosetests" tests="2" errors="0" failures="1" skip="0"><testcase classname="functional.test_toolbox.TestForTool_seqtk_comp" name="test_tool_000000" time="13.313"></testcase><testcase classname="functional.test_toolbox.TestForTool_seqtk_comp" name="test_tool_000001" time="12.937"><failure type="functional.test_toolbox.JobOutputsError" message="History item different than expected, difference (using diff): ( /home/hxr/work/tools-iuc/tools/seqtk/test-data/seqtk_cutn.out v. /tmp/tmpCMllB5/tmp/tmpJSB4jxseqtk_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 -------------------- >> begin captured logging << -------------------- requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 3 galaxy.tools.execute: DEBUG: Tool [upload1] created job [3] (698.515 ms) requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: (3) Working directory for job is: /tmp/tmpCMllB5/job_working_directory/000/3 galaxy.jobs.handler: DEBUG: (3) Dispatching to local runner requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local) galaxy.jobs.runners: DEBUG: Job [3] queued (1343.475 ms) galaxy.jobs.handler: INFO: (3) Job dispatched galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'samtools' galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring galaxy.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" galaxy.jobs.runners.local: DEBUG: (3) executing job script: /tmp/tmpCMllB5/job_working_directory/000/3/galaxy_3.sh galaxy.jobs: DEBUG: (3) Persisting job destination (destination id: local) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpCMllB5/job_working_directory/000/3/galaxy_3.sh requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 3 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: job 3 ended (finish() executed in (1640.542 ms)) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.tools.actions: INFO: Handled output (441.631 ms) galaxy.tools.actions: INFO: Verified access to datasets (9.077 ms) galaxy.tools.execute: DEBUG: Tool [seqtk_comp] created job [4] (957.828 ms) requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: (4) Working directory for job is: /tmp/tmpCMllB5/job_working_directory/000/4 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None galaxy.jobs.handler: DEBUG: (4) Dispatching to local runner galaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local) requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs.runners: DEBUG: Job [4] queued (268.598 ms) galaxy.jobs.handler: INFO: (4) Job dispatched galaxy.tools.deps: DEBUG: Building dependency shell command for dependency 'seqtk' galaxy.tools.deps: WARNING: Failed to resolve dependency on 'seqtk', ignoring galaxy.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" galaxy.jobs.runners.local: DEBUG: (4) executing job script: /tmp/tmpCMllB5/job_working_directory/000/4/galaxy_4.sh galaxy.jobs: DEBUG: (4) Persisting job destination (destination id: local) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None galaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmpCMllB5/job_working_directory/000/4/galaxy_4.sh galaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 4 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost galaxy.jobs: DEBUG: job 4 ended (finish() executed in (638.998 ms)) requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?full=true&key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/jobs/8155e4b4bf1581ff?key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/5729865256bc2525/contents/8155e4b4bf1581ff/display?raw=true&key=f638cb8a63abd80cd458910c0e8128d6 HTTP/1.1" 200 None base.twilltestcase: DEBUG: keepoutdir: /tmp/tmpCMllB5/jobfiles, ofn: /tmp/tmpCMllB5/jobfiles/seqtk_cutn.out base.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmpCMllB5/jobfiles. saved /tmp/tmpCMllB5/jobfiles/seqtk_cutn.out base.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 --------------------- >> end captured logging << ---------------------"><![CDATA[ File "/usr/lib/python2.7/unittest/case.py", line 329, in run - testMethod() - File "/home/hxr/work/galaxy/test/functional/test_toolbox.py", line 289, in test_tool - self.do_it( td ) - File "/home/hxr/work/galaxy/test/functional/test_toolbox.py", line 73, in do_it - raise e -'History item different than expected, difference (using diff):\n( /home/hxr/work/tools-iuc/tools/seqtk/test-data/seqtk_cutn.out v. /tmp/tmpCMllB5/tmp/tmpJSB4jxseqtk_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\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 << ---------------------']]></failure><system-err><![CDATA[---------------------- >> begin tool stdout << ----------------------- - ------------------------ >> end tool stdout << ------------------------ - ----------------------- >> begin tool stderr << ----------------------- - ------------------------ >> end tool stderr << ------------------------ - -]]></system-err></testcase></testsuite> \ No newline at end of file
--- 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 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml"> -<head> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta http-equiv="Content-Style-Type" content="text/css" /> - <meta name="generator" content="pandoc" /> - <title></title> - <style type="text/css">code{white-space: pre;}</style> -</head> -<body> -<h1 id="tool-test-results-powered-by-planemo">Tool Test Results (powered by Planemo)</h1> -<h2 id="executive-summary">Executive Summary</h2> -<table> -<thead> -<tr class="header"> -<th align="left">Test State</th> -<th align="left">Count</th> -</tr> -</thead> -<tbody> -<tr class="odd"> -<td align="left">Total</td> -<td align="left">2</td> -</tr> -<tr class="even"> -<td align="left">Passed</td> -<td align="left">1</td> -</tr> -<tr class="odd"> -<td align="left">Error</td> -<td align="left">0</td> -</tr> -<tr class="even"> -<td align="left">Failure</td> -<td align="left">0</td> -</tr> -<tr class="odd"> -<td align="left">Skipped</td> -<td align="left">0</td> -</tr> -</tbody> -</table> -<h2 id="detailed-results">Detailed Results</h2> -<h3 id="functional.test_toolbox.testfortool_seqtk_comp.test_tool_000000">functional.test_toolbox.TestForTool_seqtk_comp.test_tool_000000</h3> -<p>Job Passed</p> -<h3 id="functional.test_toolbox.testfortool_seqtk_comp.test_tool_000001">functional.test_toolbox.TestForTool_seqtk_comp.test_tool_000001</h3> -<p>Job Error! (State: failure)</p> -<p>Command Line:</p> -<pre class="console"><code>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</code></pre> -<p>exited with code 0.</p> -<h4 id="test-output">Test Output</h4> -<pre class="console"><code>[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']</code></pre> -</body> -</html>
--- 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 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="seqtk" version="1.0-r75-dirty"> - <repository changeset_revision="f059064a6de2" name="package_seqtk_1_0_r75" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- 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 - -``` - - - - -
--- 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 -