| Previous changeset 4:0897308ec0e5 (2018-02-14) Next changeset 6:d619e2a0a4f6 (2018-04-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173 |
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modified:
chimera.pintail.xml macros.xml |
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removed:
tool_test_output_all.html |
| b |
| diff -r 0897308ec0e5 -r 2fce0dddaa48 chimera.pintail.xml --- a/chimera.pintail.xml Wed Feb 14 12:01:42 2018 -0500 +++ b/chimera.pintail.xml Tue Mar 20 14:00:44 2018 -0400 |
| b |
| @@ -84,6 +84,7 @@ help="Default is set to 300. Note, changing the window size will require new quantile files to be made."/> <param argument="increment" type="integer" value="25" label="increment - Increment for window slide on each iteration (uses default if < 1)" help="Default is 25. Note, changing the increment will require new quantile files to be made."/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -105,6 +106,7 @@ <param name="window" value="200"/> <output name="pintail.chimeras" md5="644fe23ee459a76de7b225e530361865" ftype="txt"/> <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos" ftype="mothur.accnos"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> @@ -121,6 +123,7 @@ </output> <output name="out_quantile" md5="74372024214704010aed4f9c8258f77b" ftype="mothur.quan"/> <output name="out_freq" md5="2d2c4066c5de06c8d1d78ee3784daa3d" ftype="mothur.freq"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> |
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| diff -r 0897308ec0e5 -r 2fce0dddaa48 macros.xml --- a/macros.xml Wed Feb 14 12:01:42 2018 -0500 +++ b/macros.xml Tue Mar 20 14:00:44 2018 -0400 |
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| @@ -124,8 +124,13 @@ <xml name="param-printlevel"> <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" /> </xml> + <xml name="param-savelog"> + <param name="savelog" type="boolean" checked="false" label="Output logfile?"/> + </xml> <xml name="logfile-output"> - <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/> + <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"> + <filter>savelog</filter> + </data> </xml> <!-- Output file tests --> |
| b |
| diff -r 0897308ec0e5 -r 2fce0dddaa48 tool_test_output_all.html --- a/tool_test_output_all.html Wed Feb 14 12:01:42 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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ln -s \'/tmp/saskia/tmpKSDp0p/files/003/dataset_3926.dat\' input_otu.dat && echo \'venn( list=input_otu.dat, abund=10, calc=sobs-chao-ace, fontsize=24, sharedotus=true )\' | sed \'s/ //g\' | mothur | tee mothur.out.log", "exit_code": 0, "state": "ok", "create_time": "2018-02-08T18:54:39.400697", "params": {"sharedotus": "\\"true\\"", "nseqs": "\\"false\\"", "dbkey": "\\"hg17\\"", "fontsize": "\\"24\\"", "input": "{\\"abund\\": \\"10\\", \\"label\\": null, \\"source\\": \\"similarity\\", \\"__current_case__\\": 1, \\"calc\\": [\\"sobs\\", \\"chao\\", \\"ace\\"], \\"otu\\": {\\"values\\": [{\\"src\\": \\"hda\\", \\"id\\": 3926}]}}", "chromInfo": "\\"/tmp/saskia/tmpKSDp0p/galaxy-dev/tool-data/shared/ucsc/chrom/hg17.len\\"", "permute": "\\"4\\""}, "stderr": "mothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\\nmothur: /home/saskia/miniconda3/envs/__mothur@1.39.5/bin/../lib/libtinfo.so.5: no version information available (required by /lib/x86_64-linux-gnu/libreadline.so.6)\\n", "job_metrics": [], "model_class": "Job", "external_id": "9316", "id": "ec7711f2346cbca2", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_mothur_venn.test_tool_000001", "has_data": true}], "version": "0.1", "exit_code": 1, "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 305}};\n- renderTestResults(test_data);\n- }\n- </script>\n- </body>\n-</html>\n\\ No newline at end of file\n' |