| Previous changeset 12:15646e937936 (2017-04-07) Next changeset 14:363cce459fff (2018-02-13) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 |
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modified:
README.rst abims_xcms_xcmsSet.xml destinations_input_type.py job_conf.xml.sample macros.xml |
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| diff -r 15646e937936 -r c934dd5c49a9 README.rst --- a/README.rst Fri Apr 07 07:35:01 2017 -0400 +++ b/README.rst Wed Nov 29 09:45:19 2017 -0500 |
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| @@ -13,15 +13,19 @@ **How** - - The file `destinations_input_type.py` (shiped with this tool) must be place in `lib/galaxy/jobs/rules/` - - The `job_conf.xml` must be inspired by the `job_conf.xml.sample` shiped with this tool - - The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py` - - Restart Galaxy +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/` +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 +3. The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py` +4. Restart Galaxy Changelog/News -------------- +**Version 2.1.1 - 29/11/2017** + +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C + **Version 2.1.0 - 22/02/2017** - 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". |
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| diff -r 15646e937936 -r c934dd5c49a9 abims_xcms_xcmsSet.xml --- a/abims_xcms_xcmsSet.xml Fri Apr 07 07:35:01 2017 -0400 +++ b/abims_xcms_xcmsSet.xml Wed Nov 29 09:45:19 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0"> +<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.1"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> <macros> @@ -557,6 +557,10 @@ Changelog/News -------------- +**Version 2.1.1 - 29/11/2017** + +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C + **Version 2.1.0 - 22/02/2017** - 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". @@ -593,7 +597,7 @@ - TEST: refactoring to feed the new report tool -**Version 2.0.2 - 18/01/2016 +**Version 2.0.2 - 18/01/2016** - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. |
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| diff -r 15646e937936 -r c934dd5c49a9 destinations_input_type.py --- a/destinations_input_type.py Fri Apr 07 07:35:01 2017 -0400 +++ b/destinations_input_type.py Wed Nov 29 09:45:19 2017 -0500 |
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| @@ -18,6 +18,6 @@ input_extension = inp_data[ "input" ].extension log.debug("The input extension is %s" % input_extension) if input_extension in ["mzxml","mzml","mzdata","netcdf"]: - return 'thread1-men_free10' + return 'thread1-mem_free10' else: # zip file return 'thread4-men_free10' |
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| diff -r 15646e937936 -r c934dd5c49a9 job_conf.xml.sample --- a/job_conf.xml.sample Fri Apr 07 07:35:01 2017 -0400 +++ b/job_conf.xml.sample Wed Nov 29 09:45:19 2017 -0500 |
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| @@ -2,7 +2,6 @@ <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> <job_conf> <plugins> - <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="sge" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" type="runner"/> <plugin id="dynamic" type="runner" > <param id="rules_module">galaxy.jobs.rules</param> @@ -12,11 +11,10 @@ <handler id="main"/> </handlers> <destinations default="sge_default"> - <destination id="local" runner="local"/> <destination id="sge_default" runner="sge"> <param id="nativeSpecification">-V -w n -q galaxy.q</param> </destination> - + <destination id="thread1-men_free10" runner="sge"> <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 1 -R y -l mem_free=10G </param> </destination> @@ -31,6 +29,5 @@ </destinations> <tools> <tool destination="python_destination_input_type" id="abims_xcms_xcmsSet" /> - <tool destination="local" id="upload1"/> </tools> </job_conf> |
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| diff -r 15646e937936 -r c934dd5c49a9 macros.xml --- a/macros.xml Fri Apr 07 07:35:01 2017 -0400 +++ b/macros.xml Wed Nov 29 09:45:19 2017 -0500 |
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| @@ -19,7 +19,7 @@ </xml> <token name="@COMMAND_XCMS_SCRIPT@"> - LANG=C Rscript $__tool_directory__/xcms.r + LC_ALL=C Rscript $__tool_directory__/xcms.r </token> <token name="@COMMAND_LOG_EXIT@"> |