xcms_xcmsset: README.rst annotate

annotate README.rst @ 16:f28041d2180a draft

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

author	lecorguille
date	Mon, 30 Jan 2017 08:51:01 -0500
parents	1a9bbd4670e8
children	602acc32b549

rev	line source
4 4509e9dd03e4 planemo upload lecorguille parents: diff changeset	1
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	2 Changelog/News
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	3 --------------
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	4
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	5 Version 2.0.11 - 22/12/2016
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	6
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	7 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	8
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	9 Version 2.0.10 - 22/12/2016
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	10
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 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
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	12
13 68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 9 diff changeset	13 Version 2.0.9 - 06/07/2016
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 9 diff changeset	14
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 9 diff changeset	15 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 9 diff changeset	16
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	17 Version 2.0.8 - 06/04/2016
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	18
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	19 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	20
4 4509e9dd03e4 planemo upload lecorguille parents: diff changeset	21
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	22 Version 2.0.7 - 10/02/2016
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	23
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	24 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	25
4509e9dd03e4 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
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	27
4509e9dd03e4 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
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	29
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	30 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	31
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	32 - UPDATE: refactoring to feed the new report tool
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	33
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	34
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	35 Version 2.0.2 - 18/01/2016
4 4509e9dd03e4 planemo upload lecorguille parents: diff changeset	36
4509e9dd03e4 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.
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	38
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	39
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	40 Version 2.0.2 - 09/10/2015
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	41
4509e9dd03e4 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.
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	43
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	44
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	45 Version 2.0.2 - 02/06/2015
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	46
4509e9dd03e4 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.
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	48
4509e9dd03e4 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.
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	50
4509e9dd03e4 planemo upload lecorguille parents: diff changeset	51 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	52
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	53
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	54 Test Status
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	55 -----------
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	56
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	57 Planemo test using conda: passed
9 32cbf37cfee2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 8 diff changeset	58
8 9c3e676f7c6c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c lecorguille parents: 6 diff changeset	59 Planemo test using source env.sh: passed
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	60
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	61 Planemo shed_test : passed

Mercurial > repos > lecorguille > xcms_xcmsset

annotate README.rst @ 16:f28041d2180a draft