changeset 28:378ddb410225 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4dc5751176d47d41fa1dec33eb443e335a1a316f

--- a/abims_xcms_xcmsSet.xml	Tue Apr 30 04:41:11 2019 -0400
+++ b/abims_xcms_xcmsSet.xml	Fri Jul 26 10:26:24 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 04:41:11 2019 -0400
+++ b/destinations_input_type.py	Fri Jul 26 10:26:24 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'