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comparison readme.md @ 15:c940abd8d622 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:04:01 +0000
parents 36c84cb92e46
children 5369624840b9
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14:d98117e7b3b2 15:c940abd8d622
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