comparison readme.md @ 15:1a709ba66f2f draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

14:a3fc834f23ba

Note that, due to its size, the test data is excluded from this repository. In
order to generate the test data on call `test-data.sh`.

Manual updates should only be done to

- the `@GALAXY_VERSION@"` token in `macros.xml`
- and the manually contributed tests in `macros_test.xml` (The goal is that all
  tools that do not have an automatically generated test are covered here)
- the `hardcoded_params.json` files

In a few cases patches may be acceptable.

Installation
============

The tools work by:

Preprocessing:

- For each input / output data set parameter a directory is crated (named by
  the parameter)
- For input data set parameters the links to the actual location of the data
  sets are created

Main:

- The galaxy wrapper create two json config files: one containing the
  parameters and the values chosen by the user and the other the values of

15:1a709ba66f2f

Note that, due to its size, the test data is excluded from this repository. In
order to generate the test data on call `test-data.sh`.

Manual updates should only be done to

- and the manually contributed tests in `macros_test.xml` (The goal is that all
  tools that do not have an automatically generated test are covered here)
- the `hardcoded_params.json` files

Wrapper versions are managed in `bump.json`. For tools listed in the file
the wrapper version will be set accordingly and otherwise `0` is used. 
For a major update of the tool version the bump file should be reset (to `{}`).

In a few cases patches may be acceptable.

Installation
============

The tools work by:

Preprocessing:

- For input data set parameters the links to the actual location of the data
  sets are created, the link names are `element_identifier`.`EXT`, where `EXT`
  is an extension that is known by OpenMS
- In order to avoid name collisions for the created links each is placed in a
  unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name
  of the parameter and `DATASET_ID` is the id of the Galaxy dataset 
- the same happens for output parameters that are in 1:1 correspondence with
  an input parameter


Main:

- The galaxy wrapper create two json config files: one containing the
  parameters and the values chosen by the user and the other the values of