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I have a development galaxy at revision 1655 ... I change the name of the output files in an exec_before_job_hook, but names are not set in the workspace for parent or child files.

Hook Code

from galaxy import datatypes

def exec_before_job(app, inp_data, out_data, param_dict, tool=None):
    """Sets the name of the data"""
    job_name = param_dict.get( 'out_prefix', 'rgQCdefault' )
    html = ['html','%s_QC_report.html' % job_name]
    log = ['text','%s_QC_report.log' % job_name]
    marker = ['tabular','%s_marker.xls' % job_name]
    subj = ['tabular','%s_subject.xls' % job_name]
    het = ['tabular','%s_nhet.xls' % job_name]
    lookup={}
    lookup['html_file'] = html
    lookup['log_file'] = log
    lookup['marker_file'] = marker
    lookup['subject_file'] = subj
    lookup['het_file'] = het
    for name in lookup.keys():
        data = out_data[name]
        data_type,newname = lookup[name]
        data = app.datatypes_registry.change_datatype(data, data_type)
        data.name = newname
        out_data[name] = data