Mercurial > repos > lecorguille > xcms_xcmsset
changeset 46:bea0471f41b9 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f
| author | workflow4metabolomics |
|---|---|
| date | Fri, 26 Jul 2019 10:26:01 -0400 |
| parents | 6f9224f32a34 |
| children | 7fef3b369795 |
| files | abims_xcms_xcmsSet.xml destinations_input_type.py repository_dependencies.xml |
| diffstat | 3 files changed, 19 insertions(+), 15 deletions(-) [+] |
line wrap: on
line diff
--- a/abims_xcms_xcmsSet.xml Tue Apr 30 05:13:39 2019 -0400 +++ b/abims_xcms_xcmsSet.xml Fri Jul 26 10:26:01 2019 -0400 @@ -395,11 +395,12 @@ Description ----------- -This tool is used for preprocessing data from multiple LC/MS files (NetCDF, mzXML and mzData formats) using the xcms_ R package. It extracts ions from each sample independently, and using a statistical model, peaks are filtered and integrated. -A tutorial on how to perform xcms preprocessing is available here_. +This tool is used for preprocessing data from multiple LC/MS files (NetCDF, mzXML and mzData formats) using the xcms_ R package. +It extracts ions from each sample independently, and using a statistical model, peaks are filtered and integrated. +A tutorial on how to perform xcms preprocessing is available as GTN_ (Galaxy Training Network). .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html -.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf +.. _GTN: https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/tutorial.html -----------------
--- a/destinations_input_type.py Tue Apr 30 05:13:39 2019 -0400 +++ b/destinations_input_type.py Fri Jul 26 10:26:01 2019 -0400 @@ -1,25 +1,28 @@ -from galaxy.jobs import JobDestination import logging -import os + ''' This file must be placed in lib/galaxy/jobs/rules/ ''' + def input_type(job): ''' - This function checks the input file format/extension and decide which destination in the job_conf.xml using - - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) - - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) + This function checks the input file format/extension and decide which + destination in the job_conf.xml using + - If it's a zip file, we will launch the job in multi-thread mode + (-pe thread 8) + - If it's an individual file (mzxml, mzml, mzdata or netcdf), + the job will use for instance (-pe thread 1) ''' log = logging.getLogger(__name__) - inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) - inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) - input_extension = inp_data[ "input" ].extension - if 'input' in inp_data: - input_extension = inp_data[ "input" ].extension + indata = dict([(da.name, da.dataset) for da in job.input_datasets]) + indata.update([(da.name, da.dataset) for da in job.input_library_datasets]) + input_extension = indata["input"].extension + if 'input' in indata: + input_extension = indata["input"].extension log.debug("The input extension is %s" % input_extension) - if input_extension in ["mzxml","mzml","mzdata","netcdf"]: + if input_extension in ["mzxml", "mzml", "mzdata", "netcdf"]: return 'thread1-mem_free8' # zip file return 'thread8-mem_free16'
--- a/repository_dependencies.xml Tue Apr 30 05:13:39 2019 -0400 +++ b/repository_dependencies.xml Fri Jul 26 10:26:01 2019 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="fcc646bbf366" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> + <repository changeset_revision="3179e95069ae" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> <repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/> </repositories> \ No newline at end of file