xcms_xcmsset: README.rst annotate

annotate README.rst @ 11:91311aa08cdc draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093

author	lecorguille
date	Mon, 30 Jan 2017 08:52:59 -0500
parents	69eb0fc05837
children	15646e937936

rev	line source
5 588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	1
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	2 Changelog/News
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	3 --------------
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	4
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	5 Version 2.0.11 - 22/12/2016
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	6
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	7 - BUGFIX: propose scanrange for all methods
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	8
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	9 Version 2.0.10 - 22/12/2016
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	10
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	11 - 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	12
10 69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	13 Version 2.0.9 - 06/07/2016
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	14
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 6 diff changeset	15 - 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	16
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	17 Version 2.0.8 - 06/04/2016
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	18
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	19 - 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	20
5 588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	21
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	22 Version 2.0.7 - 10/02/2016
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	23
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	24 - BUGFIX: better management of errors. Datasets remained green although the process failed
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	25
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	26 - 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	27
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	28 - 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	29
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	30 - UPDATE: refactoring of internal management of inputs/outputs
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	31
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	32 - UPDATE: refactoring to feed the new report tool
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	33
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	34
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	35 Version 2.0.2 - 18/01/2016
5 588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	36
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	37 - 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	38
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	39
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	40 Version 2.0.2 - 09/10/2015
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	41
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	42 - 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	43
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	44
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	45 Version 2.0.2 - 02/06/2015
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	46
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	47 - 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	48
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	49 - 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	50
588b0a7ae4b0 planemo upload lecorguille parents: diff changeset	51 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	52
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	53
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	54 Test Status
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	55 -----------
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	56
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	57 Planemo test using conda: passed
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	58
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	59 Planemo test using source env.sh: passed
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	60
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	61 Planemo shed_test : passed

Mercurial > repos > lecorguille > xcms_xcmsset

annotate README.rst @ 11:91311aa08cdc draft