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Target draft 3 of CWL instead of draft 2.

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jmchilton committed Apr 18, 2016
1 parent 302886c commit 775bf49bdc6abc67390feffea1988e71115dcd0b
Showing with 54,778 additions and 885 deletions.
  1. +2 −2 README.rst
  2. +0 −34 project_templates/cwl_draft2_spec/add-lines-wf.cwl
  3. +0 −28 project_templates/cwl_draft2_spec/cat1-tool.cwl
  4. +0 −23 project_templates/cwl_draft2_spec/cat2-tool.cwl
  5. +0 −29 project_templates/cwl_draft2_spec/cat3-tool.cwl
  6. +0 −33 project_templates/cwl_draft2_spec/cat4-tool.cwl
  7. +0 −33 project_templates/cwl_draft2_spec/cat5-tool.cwl
  8. +0 −25 project_templates/cwl_draft2_spec/count-lines1-wf.cwl
  9. +0 −41 project_templates/cwl_draft2_spec/count-lines2-wf.cwl
  10. +0 −24 project_templates/cwl_draft2_spec/count-lines4-wf.cwl
  11. +0 −25 project_templates/cwl_draft2_spec/count-lines6-wf.cwl
  12. +0 −21 project_templates/cwl_draft2_spec/count-lines7-wf.cwl
  13. +0 −22 project_templates/cwl_draft2_spec/count-lines8-wf.cwl
  14. +0 −27 project_templates/cwl_draft2_spec/count-lines9-wf.cwl
  15. +0 −20 project_templates/cwl_draft2_spec/env-tool1.cwl
  16. +0 −20 project_templates/cwl_draft2_spec/env-tool2.cwl
  17. +0 −25 project_templates/cwl_draft2_spec/env-wf1.cwl
  18. +0 −25 project_templates/cwl_draft2_spec/env-wf2.cwl
  19. +0 −10 project_templates/cwl_draft2_spec/node-engine.cwl
  20. +0 −16 project_templates/cwl_draft2_spec/parseInt-tool.cwl
  21. +0 −23 project_templates/cwl_draft2_spec/rename.cwl
  22. +0 −36 project_templates/cwl_draft2_spec/revtool.cwl
  23. +0 −84 project_templates/cwl_draft2_spec/search.cwl
  24. +0 −34 project_templates/cwl_draft2_spec/sorttool.cwl
  25. +0 −27 project_templates/cwl_draft2_spec/template-tool.cwl
  26. +0 −17 project_templates/cwl_draft2_spec/wc-tool.cwl
  27. +0 −19 project_templates/cwl_draft2_spec/wc2-tool.cwl
  28. +51,294 −0 project_templates/cwl_draft3_spec/EDAM.owl
  29. +3 −0 project_templates/cwl_draft3_spec/abc.json
  30. +4 −3 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/binding-test.cwl
  31. +1 −5 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/bwa-mem-job.json
  32. +18 −17 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/bwa-mem-tool.cwl
  33. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/cat-job.json
  34. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/cat-n-job.json
  35. +18 −0 project_templates/cwl_draft3_spec/cat1-tool.cwl
  36. +13 −0 project_templates/cwl_draft3_spec/cat2-tool.cwl
  37. +19 −0 project_templates/cwl_draft3_spec/cat3-tool.cwl
  38. +18 −0 project_templates/cwl_draft3_spec/cat4-tool.cwl
  39. +21 −0 project_templates/cwl_draft3_spec/cat5-tool.cwl
  40. +4 −0 project_templates/cwl_draft3_spec/conflict-job.json
  41. +80 −0 project_templates/cwl_draft3_spec/conflict-wf.cwl
  42. +26 −0 project_templates/cwl_draft3_spec/count-lines1-wf.cwl
  43. +41 −0 project_templates/cwl_draft3_spec/count-lines2-wf.cwl
  44. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/count-lines3-job.json
  45. +10 −8 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/count-lines3-wf.cwl
  46. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/count-lines4-job.json
  47. +26 −0 project_templates/cwl_draft3_spec/count-lines4-wf.cwl
  48. +9 −7 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/count-lines5-wf.cwl
  49. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/count-lines6-job.json
  50. +27 −0 project_templates/cwl_draft3_spec/count-lines6-wf.cwl
  51. +25 −0 project_templates/cwl_draft3_spec/count-lines7-wf.cwl
  52. +23 −0 project_templates/cwl_draft3_spec/count-lines8-wf.cwl
  53. +28 −0 project_templates/cwl_draft3_spec/count-lines9-wf.cwl
  54. +1,077 −0 project_templates/cwl_draft3_spec/dcterms.rdf
  55. +5 −6 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/echo-tool.cwl
  56. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/empty.json
  57. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/env-job.json
  58. +19 −0 project_templates/cwl_draft3_spec/env-tool1.cwl
  59. +19 −0 project_templates/cwl_draft3_spec/env-tool2.cwl
  60. +26 −0 project_templates/cwl_draft3_spec/env-wf1.cwl
  61. +26 −0 project_templates/cwl_draft3_spec/env-wf2.cwl
  62. +609 −0 project_templates/cwl_draft3_spec/foaf.rdf
  63. +7 −0 project_templates/cwl_draft3_spec/formattest-job.json
  64. +20 −0 project_templates/cwl_draft3_spec/formattest.cwl
  65. +7 −0 project_templates/cwl_draft3_spec/formattest2-job.json
  66. +23 −0 project_templates/cwl_draft3_spec/formattest2.cwl
  67. +25 −0 project_templates/cwl_draft3_spec/formattest3.cwl
  68. +20 −0 project_templates/cwl_draft3_spec/glob-expr-list.cwl
  69. +7 −0 project_templates/cwl_draft3_spec/gx_edam.ttl
  70. BIN project_templates/cwl_draft3_spec/hello.tar
  71. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/hello.txt
  72. +7 −1 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/index.py
  73. +32 −0 project_templates/cwl_draft3_spec/metadata.cwl
  74. +3 −0 project_templates/cwl_draft3_spec/null-expression1-job.json
  75. +14 −0 project_templates/cwl_draft3_spec/null-expression1-tool.cwl
  76. +3 −0 project_templates/cwl_draft3_spec/null-expression2-job.json
  77. +14 −0 project_templates/cwl_draft3_spec/null-expression2-tool.cwl
  78. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/number.txt
  79. +26 −0 project_templates/cwl_draft3_spec/optional-output.cwl
  80. +16 −0 project_templates/cwl_draft3_spec/params.cwl
  81. +19 −0 project_templates/cwl_draft3_spec/params2.cwl
  82. +110 −0 project_templates/cwl_draft3_spec/params_inc.yml
  83. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/parseInt-job.json
  84. +14 −0 project_templates/cwl_draft3_spec/parseInt-tool.cwl
  85. +6 −0 project_templates/cwl_draft3_spec/record-output-job.json
  86. +38 −0 project_templates/cwl_draft3_spec/record-output.cwl
  87. +10 −0 project_templates/cwl_draft3_spec/ref.fasta
  88. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/rename-job.json
  89. +17 −0 project_templates/cwl_draft3_spec/rename.cwl
  90. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/revsort-job.json
  91. +18 −15 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/revsort.cwl
  92. +37 −0 project_templates/cwl_draft3_spec/revtool.cwl
  93. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/scatter-job1.json
  94. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/scatter-job2.json
  95. +7 −0 project_templates/cwl_draft3_spec/scatter-valuefrom-job1.json
  96. +4 −0 project_templates/cwl_draft3_spec/scatter-valuefrom-job2.json
  97. +55 −0 project_templates/cwl_draft3_spec/scatter-valuefrom-wf1.cwl
  98. +70 −0 project_templates/cwl_draft3_spec/scatter-valuefrom-wf2.cwl
  99. +66 −0 project_templates/cwl_draft3_spec/scatter-valuefrom-wf3.cwl
  100. +64 −0 project_templates/cwl_draft3_spec/scatter-valuefrom-wf4.cwl
  101. +17 −18 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/scatter-wf1.cwl
  102. +22 −23 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/scatter-wf2.cwl
  103. +19 −18 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/scatter-wf3.cwl
  104. +18 −19 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/scatter-wf4.cwl
  105. +6 −0 project_templates/cwl_draft3_spec/schemadef-job.json
  106. +21 −0 project_templates/cwl_draft3_spec/schemadef-tool.cwl
  107. +9 −0 project_templates/cwl_draft3_spec/schemadef-type.yml
  108. +23 −0 project_templates/cwl_draft3_spec/schemadef-wf.cwl
  109. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/search-job.json
  110. +101 −0 project_templates/cwl_draft3_spec/search.cwl
  111. +1 −2 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/search.py
  112. +21 −0 project_templates/cwl_draft3_spec/shelltest.cwl
  113. +35 −0 project_templates/cwl_draft3_spec/sorttool.cwl
  114. +1 −0 project_templates/cwl_draft3_spec/step-valuefrom-job.json
  115. +34 −0 project_templates/cwl_draft3_spec/step-valuefrom-wf.cwl
  116. +8 −0 project_templates/cwl_draft3_spec/step-valuefrom-wf.json
  117. +42 −0 project_templates/cwl_draft3_spec/step-valuefrom2-wf.cwl
  118. +43 −0 project_templates/cwl_draft3_spec/step-valuefrom3-wf.cwl
  119. +19 −0 project_templates/cwl_draft3_spec/template-tool.cwl
  120. +18 −0 project_templates/cwl_draft3_spec/test-cwl-out.cwl
  121. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/tmap-job.json
  122. +11 −12 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/tmap-tool.cwl
  123. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/underscore.js
  124. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/wc-job.json
  125. +15 −0 project_templates/cwl_draft3_spec/wc-tool.cwl
  126. +17 −0 project_templates/cwl_draft3_spec/wc2-tool.cwl
  127. +4 −6 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/wc3-tool.cwl
  128. +21 −0 project_templates/cwl_draft3_spec/wc4-tool.cwl
  129. 0 project_templates/{cwl_draft2_spec → cwl_draft3_spec}/whale.txt
  130. +2 −2 tests/test_cwl_run.py
@@ -289,8 +289,8 @@ CWL tools.

::

% planemo project_init --template cwl_draft2_spec
% planemo serve --cwl cwl_draft2_spec/cat1-tool.cwl
% planemo project_init --template cwl_draft3_spec
% planemo serve --cwl cwl_draft3_spec/cat1-tool.cwl

.. _Galaxy: http://galaxyproject.org/
.. _GitHub: https://github.com/

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