Mercurial > repos > devteam > basecoverage
changeset 3:0a3e3133b09d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:47:11 -0500 |
| parents | b8a9e718caa3 |
| children | 2cedec3759e4 |
| files | gops_basecoverage.py operation_filter.py tool_dependencies.xml |
| diffstat | 3 files changed, 26 insertions(+), 44 deletions(-) [+] |
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--- a/gops_basecoverage.py Mon Apr 14 09:01:22 2014 -0400 +++ b/gops_basecoverage.py Wed Nov 11 12:47:11 2015 -0500 @@ -6,34 +6,32 @@ -1, --cols1=N,N,N,N: Columns for start, end, strand in first file """ -import sys, traceback, fileinput -from warnings import warn -from bx.intervals import * -from bx.intervals.io import * -from bx.intervals.operations.base_coverage import * +import fileinput +import sys +from bx.intervals.io import NiceReaderWrapper +from bx.intervals.operations.base_coverage import base_coverage from bx.cookbook import doc_optparse -from galaxy.tools.util.galaxyops import * +from bx.tabular.io import ParseError +from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped assert sys.version_info[:2] >= ( 2, 4 ) + def main(): - upstream_pad = 0 - downstream_pad = 0 - options, args = doc_optparse.parse( __doc__ ) try: chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) in_fname, out_fname = args except: doc_optparse.exception() - + g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ), chrom_col=chr_col_1, start_col=start_col_1, end_col=end_col_1, - strand_col = strand_col_1, + strand_col=strand_col_1, fix_strand=True ) - + try: bases = base_coverage(g1) except ParseError, exc:
--- a/operation_filter.py Mon Apr 14 09:01:22 2014 -0400 +++ b/operation_filter.py Wed Nov 11 12:47:11 2015 -0500 @@ -1,7 +1,4 @@ # runs after the job (and after the default post-filter) -import os -from galaxy import eggs -from galaxy import jobs from galaxy.tools.parameters import DataToolParameter from galaxy.jobs.handler import JOB_ERROR @@ -12,11 +9,6 @@ except: from sets import Set as set -#def exec_before_process(app, inp_data, out_data, param_dict, tool=None): -# """Sets the name of the data""" -# dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] ) -# if len(dbkeys) != 1: -# raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>' def validate_input( trans, error_map, param_values, page_param_map ): dbkeys = set() @@ -25,7 +17,7 @@ for name, param in page_param_map.iteritems(): if isinstance( param, DataToolParameter ): # for each dataset parameter - if param_values.get(name, None) != None: + if param_values.get(name, None) is not None: dbkeys.add( param_values[name].dbkey ) data_params += 1 # check meta data @@ -34,17 +26,15 @@ if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ): # TODO: currently cannot validate GFF inputs b/c they are not derived from interval. pass - else: # Validate interval datatype. - startCol = int( param.metadata.startCol ) - endCol = int( param.metadata.endCol ) - chromCol = int( param.metadata.chromCol ) + else: # Validate interval datatype. + int( param.metadata.startCol ) + int( param.metadata.endCol ) + int( param.metadata.chromCol ) if param.metadata.strandCol is not None: - strandCol = int ( param.metadata.strandCol ) - else: - strandCol = 0 + int( param.metadata.strandCol ) except: error_msg = "The attributes of this dataset are not properly set. " + \ - "Click the pencil icon in the history item to set the chrom, start, end and strand columns." + "Click the pencil icon in the history item to set the chrom, start, end and strand columns." error_map[name] = error_msg data_param_names.add( name ) if len( dbkeys ) > 1: @@ -55,38 +45,33 @@ for name in data_param_names: error_map[name] = "A dataset of the appropriate type is required" + # Commented out by INS, 5/30/2007. What is the PURPOSE of this? def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): """Verify the output data after each run""" - items = out_data.items() - - for name, data in items: + for data in out_data.values(): try: if stderr and len( stderr ) > 0: raise Exception( stderr ) - except Exception, exc: + except Exception: data.blurb = JOB_ERROR data.state = JOB_ERROR -## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): -## pass - def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): exec_after_process( app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr) # strip strand column if clusters were merged - items = out_data.items() - for name, data in items: - if param_dict['returntype'] == True: + for data in out_data.values(): + if param_dict['returntype'] is True: data.metadata.chromCol = 1 data.metadata.startCol = 2 data.metadata.endCol = 3 # merge always clobbers strand data.metadata.strandCol = None - + def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): exec_after_process( @@ -94,6 +79,5 @@ # strip strand column if clusters were merged if param_dict["returntype"] == '1': - items = out_data.items() - for name, data in items: + for data in out_data.values(): data.metadata.strandCol = None
--- a/tool_dependencies.xml Mon Apr 14 09:01:22 2014 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:47:11 2015 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="bx-python" version="0.7.1"> - <repository changeset_revision="41eb9d9f667d" name="package_bx_python_0_7" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2d0c08728bca" name="package_bx_python_0_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="galaxy-ops" version="1.0.0"> - <repository changeset_revision="4e39032e4ec6" name="package_galaxy_ops_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9cbb20b85c01" name="package_galaxy_ops_1_0_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>