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Implement report templates #304

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merged 1 commit into from Sep 19, 2015

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erasche commented Sep 19, 2015

I'm admittedly not exactly in love with the command line options. I'd rather have a --tool_test_output_formats switch and be able to specify one or more of (html, text, markdown, xunit, json), and deprecate --tool_test_output{'', '_xunit', '_json', '_text', '_markdown') but that would remove the nice ability to specify output file names.

Should address @peterjc's issue #302.

Example Text

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

Example Markdown

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:

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

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
Implement report templates
Provide jinja2 templates for markdown, text
@peterjc

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peterjc commented Sep 19, 2015

Looks good - I'll try to test this out this week, thanks!

@erasche erasche referenced this pull request Sep 19, 2015

Merged

Shed diff report #305

1 of 1 task complete

jmchilton added a commit that referenced this pull request Sep 19, 2015

@jmchilton jmchilton merged commit 296ae50 into master Sep 19, 2015

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jmchilton commented Sep 19, 2015

Looks good me @erasche, thanks!

@erasche erasche deleted the report-templates branch Oct 20, 2015

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