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comparison README.rst @ 12:15646e937936 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:35:01 -0400
parents 91311aa08cdc
children c934dd5c49a9
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11:91311aa08cdc 12:15646e937936
1 Job Dynamic Destination Mapping
2 -------------------------------
3
4 **Why**
5
6 xcmsSet wrapper allow both individual file and zip file which can contain several samples.
7 Thus, it can be interesting to adjust the number of thread according to the input type.
8 For example: 1 thread for a single mzXML or NetCDF file and 8 threads for a zip file.
9
10 **What**
11
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...
13
14 **How**
15
16 - The file `destinations_input_type.py` (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
17 - The `job_conf.xml` must be inspired by the `job_conf.xml.sample` shiped with this tool
18 - The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
19 - Restart Galaxy
20
1 21
2 Changelog/News 22 Changelog/News
3 -------------- 23 --------------
24
25 **Version 2.1.0 - 22/02/2017**
26
27 - 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".
28
29 - 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
4 30
5 **Version 2.0.11 - 22/12/2016** 31 **Version 2.0.11 - 22/12/2016**
6 32
7 - BUGFIX: propose scanrange for all methods 33 - BUGFIX: propose scanrange for all methods
8 34
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. 73 - 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.
48 74
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. 75 - 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.
50 76
51 - IMPROVEMENT: parameter labels have changed to facilitate their reading. 77 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
52
53
54 Test Status
55 -----------
56
57 Planemo test using conda: passed
58
59 Planemo test using source env.sh: passed
60
61 Planemo shed_test : passed