Mercurial > repos > galaxyp > openms_ticcalculator
comparison readme.md @ 13:d623ad21ca59 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:10:31 +0000 |
parents | 32667824b653 |
children | 5f36444a0f9d |
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12:4c263ca917ef | 13:d623ad21ca59 |
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20 Note that, due to its size, the test data is excluded from this repository. In | 20 Note that, due to its size, the test data is excluded from this repository. In |
21 order to generate the test data on call `test-data.sh`. | 21 order to generate the test data on call `test-data.sh`. |
22 | 22 |
23 Manual updates should only be done to | 23 Manual updates should only be done to |
24 | 24 |
25 - the `@GALAXY_VERSION@"` token in `macros.xml` | |
26 - and the manually contributed tests in `macros_test.xml` (The goal is that all | 25 - and the manually contributed tests in `macros_test.xml` (The goal is that all |
27 tools that do not have an automatically generated test are covered here) | 26 tools that do not have an automatically generated test are covered here) |
28 - the `hardcoded_params.json` files | 27 - the `hardcoded_params.json` files |
28 | |
29 Wrapper versions are managed in `bump.json`. For tools listed in the file | |
30 the wrapper version will be set accordingly and otherwise `0` is used. | |
31 For a major update of the tool version the bump file should be reset (to `{}`). | |
29 | 32 |
30 In a few cases patches may be acceptable. | 33 In a few cases patches may be acceptable. |
31 | 34 |
32 Installation | 35 Installation |
33 ============ | 36 ============ |
69 | 72 |
70 The tools work by: | 73 The tools work by: |
71 | 74 |
72 Preprocessing: | 75 Preprocessing: |
73 | 76 |
74 - For each input / output data set parameter a directory is crated (named by | |
75 the parameter) | |
76 - For input data set parameters the links to the actual location of the data | 77 - For input data set parameters the links to the actual location of the data |
77 sets are created | 78 sets are created, the link names are `element_identifier`.`EXT`, where `EXT` |
79 is an extension that is known by OpenMS | |
80 - In order to avoid name collisions for the created links each is placed in a | |
81 unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name | |
82 of the parameter and `DATASET_ID` is the id of the Galaxy dataset | |
83 - the same happens for output parameters that are in 1:1 correspondence with | |
84 an input parameter | |
85 | |
78 | 86 |
79 Main: | 87 Main: |
80 | 88 |
81 - The galaxy wrapper create two json config files: one containing the | 89 - The galaxy wrapper create two json config files: one containing the |
82 parameters and the values chosen by the user and the other the values of | 90 parameters and the values chosen by the user and the other the values of |