xcms_xcmsset: README.rst annotate

annotate README.rst @ 13:c934dd5c49a9 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1

author	lecorguille
date	Wed, 29 Nov 2017 09:45:19 -0500
parents	15646e937936
children	b62808a2a008

rev	line source
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	1 Job Dynamic Destination Mapping
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	2 -------------------------------
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	3
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	4 Why
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	5
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	6 xcmsSet wrapper allow both individual file and zip file which can contain several samples.
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	7 Thus, it can be interesting to adjust the number of thread according to the input type.
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	8 For example: 1 thread for a single mzXML or NetCDF file and 8 threads for a zip file.
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	9
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	10 What
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	11
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	12 The [Dynamic Destination Mapping](https://galaxyproject.org/admin/config/jobs/#dynamic-destination-mapping) allow Galaxy to choose a destination at runtime based on factors such as the job inputs, user submitting the job, cluster status, etc...
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	13
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	14 How
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	15
13 c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	16 1. The file [`destinations_input_type.py`](https://raw.githubusercontent.com/workflow4metabolomics/xcms/master/galaxy/xcms_xcmsset/destinations_input_type.py) (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	17 2. The `job_conf.xml` must be inspired by the [`job_conf.xml.sample`](https://github.com/workflow4metabolomics/xcms/blob/master/galaxy/xcms_xcmsset/job_conf.xml.sample) shiped with this tool
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	18 3. The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	19 4. Restart Galaxy
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	20
5 588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	21
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	22 Changelog/News
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	23 --------------
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	24
13 c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	25 Version 2.1.1 - 29/11/2017
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	26
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	27 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	28
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	29 Version 2.1.0 - 22/02/2017
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	30
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	31 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	32
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	33 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	34
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	35 Version 2.0.11 - 22/12/2016
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	36
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	37 - BUGFIX: propose scanrange for all methods
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	38
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	39 Version 2.0.10 - 22/12/2016
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	40
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	41 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	42
10 69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	43 Version 2.0.9 - 06/07/2016
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	44
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	45 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	46
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	47 Version 2.0.8 - 06/04/2016
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	48
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	49 - TEST: refactoring to pass planemo test using conda dependencies
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	50
5 588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	51
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	52 Version 2.0.7 - 10/02/2016
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	53
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	54 - BUGFIX: better management of errors. Datasets remained green although the process failed
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	55
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	56 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	57
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	58 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	59
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	60 - UPDATE: refactoring of internal management of inputs/outputs
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	61
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	62 - UPDATE: refactoring to feed the new report tool
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	63
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	64
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	65 Version 2.0.2 - 18/01/2016
5 588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	66
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	67 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	68
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	69
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	70 Version 2.0.2 - 09/10/2015
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	71
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	72 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	73
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	74
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	75 Version 2.0.2 - 02/06/2015
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	76
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	77 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	78
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	79 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	80
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	81 - IMPROVEMENT: parameter labels have changed to facilitate their reading.

Mercurial > repos > lecorguille > xcms_xcmsset

annotate README.rst @ 13:c934dd5c49a9 draft