Mercurial > repos > devteam > sicer

--- a/sicer_wrapper.py	Wed Oct 24 11:31:03 2018 -0400
+++ b/sicer_wrapper.py	Wed Oct 28 23:36:25 2020 +0000
@@ -1,157 +1,158 @@
 #!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg

 """
 A wrapper script for running SICER (spatial clustering approach for the identification of ChIP-enriched regions) region caller.
 """

-import sys, optparse, os, tempfile, subprocess, shutil
-
-CHUNK_SIZE = 2**20 #1mb
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile

-#HACK! FIXME: allow using all specified builds, would currently require hacking SICER's "GenomeData.py" on the fly.
-VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]
+CHUNK_SIZE = 2**20  # 1mb

-def cleanup_before_exit( tmp_dir ):
-    if tmp_dir and os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
+# HACK! FIXME: allow using all specified builds, would currently require hacking SICER's "GenomeData.py" on the fly.
+VALID_BUILDS = ['mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8']


-def open_file_from_option( filename, mode = 'rb' ):
+def cleanup_before_exit(tmp_dir):
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
+
+
+def open_file_from_option(filename, mode='rb'):
     if filename:
-        return open( filename, mode = mode )
+        return open(filename, mode=mode)
     return None

-def add_one_to_file_column( filename, column, split_char = "\t", startswith_skip = None ):
-    tmp_out = tempfile.TemporaryFile( mode='w+b' )
-    tmp_in = open( filename )
-    for line in tmp_in:
-        if startswith_skip and line.startswith( startswith_skip ):
-            tmp_out.write( line )
-        else:
-            fields = line.rstrip( '\n\r' ).split( split_char )
-            if len( fields ) <= column:
-                tmp_out.write( line )
-            else:
-                fields[ column ] = str( int( fields[ column ] ) + 1 )
-                tmp_out.write( "%s\n" % ( split_char.join( fields )  ) )
-    tmp_in.close()
-    tmp_out.seek( 0 )
-    tmp_in = open( filename, 'wb' )
-    while True:
-        chunk = tmp_out.read( CHUNK_SIZE )
-        if chunk:
-            tmp_in.write( chunk )
-        else:
-            break
-    tmp_in.close()
-    tmp_out.close()
+
+def add_one_to_file_column(filename, column, split_char="\t", startswith_skip=None):
+    with tempfile.NamedTemporaryFile(mode='w+b', delete=False) as tmp_out:
+        with open(filename) as fh:
+            tmp_path = tmp_out.name
+            for line in fh:
+                if startswith_skip and line.startswith(startswith_skip):
+                    tmp_out.write(line)
+                else:
+                    fields = line.rstrip('\n\r').split(split_char)
+                    if len(fields) <= column:
+                        tmp_out.write(line)
+                    else:
+                        fields[column] = str(int(fields[column]) + 1)
+                        tmp_out.write("%s\n" % (split_char.join(fields)))
+    shutil.move(tmp_path, filename)
+

 def __main__():
-    #Parse Command Line
     parser = optparse.OptionParser()
-    #stdout/err
-    parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
-    parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
-    parser.add_option( '', '--fix_off_by_one_errors', dest='fix_off_by_one_errors', action='store_true', default=False, help='If specified, fix off-by-one errors in output files' )
-    #inputs
-    parser.add_option( '-b', '--bed_file', dest='bed_file', action='store', type="string", default=None, help='Input ChIP BED file.' )
-    parser.add_option( '-c', '--control_file', dest='control_file', action='store', type="string", default=None, help='Input control BED file.' )
-    parser.add_option( '-d', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='Input dbkey.' )
-    parser.add_option( '-r', '--redundancy_threshold', dest='redundancy_threshold', action='store', type="int", default=1, help='Redundancy Threshold: The number of copies of identical reads allowed in a library.' )
-    parser.add_option( '-w', '--window_size', dest='window_size', action='store', type="int", default=200, help='Window size: resolution of SICER algorithm. For histone modifications, one can use 200 bp' )
-    parser.add_option( '-f', '--fragment_size', dest='fragment_size', action='store', type="int", default=150, help='Fragment size: is for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75.' )
-    parser.add_option( '-e', '--effective_genome_fraction', dest='effective_genome_fraction', action='store', type="float", default=0.74, help='Effective genome fraction: Effective Genome as fraction of the genome size. It depends on read length.' )
-    parser.add_option( '-g', '--gap_size', dest='gap_size', action='store', type="int", default=600, help='Gap size: needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ... .' )
-    parser.add_option( '-o', '--error_cut_off', dest='error_cut_off', action='store', type="string", default="0.1", help='Error Cut off: FDR or E-value' ) #read as string to construct names properly
-    #outputs
-    parser.add_option( '', '--redundancy_removed_test_bed_output_file', dest='redundancy_removed_test_bed_output_file', action='store', type="string", default=None, help='test-1-removed.bed: redundancy_removed test bed file' )
-    parser.add_option( '', '--redundancy_removed_control_bed_output_file', dest='redundancy_removed_control_bed_output_file', action='store', type="string", default=None, help='control-1-removed.bed: redundancy_removed control bed file' )
-    parser.add_option( '', '--summary_graph_output_file', dest='summary_graph_output_file', action='store', type="string", default=None, help='test-W200.graph: summary graph file for test-1-removed.bed with window size 200, in bedGraph format.' )
-    parser.add_option( '', '--test_normalized_wig_output_file', dest='test_normalized_wig_output_file', action='store', type="string", default=None, help='test-W200-normalized.wig: the above file normalized by library size per million and converted into wig format. This file can be uploaded to the UCSC genome browser' )
-    parser.add_option( '', '--score_island_output_file', dest='score_island_output_file', action='store', type="string", default=None, help='test-W200-G600.scoreisland: an intermediate file for debugging usage.' )
-    parser.add_option( '', '--islands_summary_output_file', dest='islands_summary_output_file', action='store', type="string", default=None, help='test-W200-G600-islands-summary: summary of all candidate islands with their statistical significance.' )
-    parser.add_option( '', '--significant_islands_summary_output_file', dest='significant_islands_summary_output_file', action='store', type="string", default=None, help='test-W200-G600-islands-summary-FDR.01: summary file of significant islands with requirement of FDR=0.01.' )
-    parser.add_option( '', '--significant_islands_output_file', dest='significant_islands_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-island.bed: delineation of significant islands in "chrom start end read-count-from-redundancy_removed-test.bed" format' )
-    parser.add_option( '', '--island_filtered_output_file', dest='island_filtered_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-islandfiltered.bed: library of raw redundancy_removed reads on significant islands.' )
-    parser.add_option( '', '--island_filtered_normalized_wig_output_file', dest='island_filtered_normalized_wig_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-islandfiltered-normalized.wig: wig file for the island-filtered redundancy_removed reads.' )
+    parser.add_option('', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.')
+    parser.add_option('', '--fix_off_by_one_errors', dest='fix_off_by_one_errors', action='store_true', default=False, help='If specified, fix off-by-one errors in output files')
+    # inputs
+    parser.add_option('-b', '--bed_file', dest='bed_file', action='store', type="string", default=None, help='Input ChIP BED file.')
+    parser.add_option('-c', '--control_file', dest='control_file', action='store', type="string", default=None, help='Input control BED file.')
+    parser.add_option('-d', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='Input dbkey.')
+    parser.add_option('-r', '--redundancy_threshold', dest='redundancy_threshold', action='store', type="int", default=1, help='Redundancy Threshold: The number of copies of identical reads allowed in a library.')
+    parser.add_option('-w', '--window_size', dest='window_size', action='store', type="int", default=200, help='Window size: resolution of SICER algorithm. For histone modifications, one can use 200 bp')
+    parser.add_option('-f', '--fragment_size', dest='fragment_size', action='store', type="int", default=150, help='Fragment size: is for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75.')
+    parser.add_option('-e', '--effective_genome_fraction', dest='effective_genome_fraction', action='store', type="float", default=0.74, help='Effective genome fraction: Effective Genome as fraction of the genome size. It depends on read length.')
+    parser.add_option('-g', '--gap_size', dest='gap_size', action='store', type="int", default=600, help='Gap size: needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ... .')
+    parser.add_option('-o', '--error_cut_off', dest='error_cut_off', action='store', type="string", default="0.1", help='Error Cut off: FDR or E-value')  # read as string to construct names properly
+    # outputs
+    parser.add_option('', '--redundancy_removed_test_bed_output_file', dest='redundancy_removed_test_bed_output_file', action='store', type="string", default=None, help='test-1-removed.bed: redundancy_removed test bed file')
+    parser.add_option('', '--redundancy_removed_control_bed_output_file', dest='redundancy_removed_control_bed_output_file', action='store', type="string", default=None, help='control-1-removed.bed: redundancy_removed control bed file')
+    parser.add_option('', '--summary_graph_output_file', dest='summary_graph_output_file', action='store', type="string", default=None, help='test-W200.graph: summary graph file for test-1-removed.bed with window size 200, in bedGraph format.')
+    parser.add_option('', '--test_normalized_wig_output_file', dest='test_normalized_wig_output_file', action='store', type="string", default=None, help='test-W200-normalized.wig: the above file normalized by library size per million and converted into wig format. This file can be uploaded to the UCSC genome browser')
+    parser.add_option('', '--score_island_output_file', dest='score_island_output_file', action='store', type="string", default=None, help='test-W200-G600.scoreisland: an intermediate file for debugging usage.')
+    parser.add_option('', '--islands_summary_output_file', dest='islands_summary_output_file', action='store', type="string", default=None, help='test-W200-G600-islands-summary: summary of all candidate islands with their statistical significance.')
+    parser.add_option('', '--significant_islands_summary_output_file', dest='significant_islands_summary_output_file', action='store', type="string", default=None, help='test-W200-G600-islands-summary-FDR.01: summary file of significant islands with requirement of FDR=0.01.')
+    parser.add_option('', '--significant_islands_output_file', dest='significant_islands_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-island.bed: delineation of significant islands in "chrom start end read-count-from-redundancy_removed-test.bed" format')
+    parser.add_option('', '--island_filtered_output_file', dest='island_filtered_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-islandfiltered.bed: library of raw redundancy_removed reads on significant islands.')
+    parser.add_option('', '--island_filtered_normalized_wig_output_file', dest='island_filtered_normalized_wig_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-islandfiltered-normalized.wig: wig file for the island-filtered redundancy_removed reads.')
     (options, args) = parser.parse_args()
-
-    #check if valid build
-    assert options.dbkey in VALID_BUILDS, ValueError( "The specified build ('%s') is not available for this tool." % options.dbkey )
-
-    #everything will occur in this temp directory
+
+    # check if valid build
+    assert options.dbkey in VALID_BUILDS, ValueError("The specified build ('%s') is not available for this tool." % options.dbkey)
+
+    # everything will occur in this temp directory
     tmp_dir = tempfile.mkdtemp()
-
-    #link input files into tmp_dir and build command line
+
+    # link input files into tmp_dir and build command line
     bed_base_filename = 'input_bed_file'
     bed_filename = '%s.bed' % bed_base_filename
-    os.symlink( options.bed_file, os.path.join( tmp_dir, bed_filename ) )
+    os.symlink(options.bed_file, os.path.join(tmp_dir, bed_filename))
     if options.control_file is not None:
         cmd = "SICER.sh"
     else:
         cmd = "SICER-rb.sh"
-    cmd = '%s "%s" "%s"' % ( cmd, tmp_dir, bed_filename )
+    cmd = '%s "%s" "%s"' % (cmd, tmp_dir, bed_filename)
     if options.control_file is not None:
         control_base_filename = 'input_control_file'
         control_filename = '%s.bed' % control_base_filename
-        os.symlink( options.control_file, os.path.join( tmp_dir, control_filename ) )
-        cmd = '%s "%s"' % ( cmd, control_filename )
-    cmd = '%s "%s" "%s" "%i" "%i" "%i" "%f" "%i" "%s"' % ( cmd, tmp_dir, options.dbkey, options.redundancy_threshold, options.window_size, options.fragment_size, options.effective_genome_fraction, options.gap_size, options.error_cut_off )
-
-    #set up stdout and stderr output options
-    stdout = open_file_from_option( options.stdout, mode = 'wb' )
-    stderr = open_file_from_option( options.stderr, mode = 'wb' )
-    #if no stderr file is specified, we'll use our own
-    if stderr is None:
-        stderr = tempfile.NamedTemporaryFile( dir=tmp_dir )
-        stderr.close()
-        stderr = open( stderr.name, 'w+b' )
-
-    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
-    return_code = proc.wait()
-
-    if return_code:
-        stderr_target = sys.stderr
-    else:
-        stderr_target = stdout #sys.stdout
-        stderr_target.write( "\nAdditionally, these warnings were reported:\n" )
-    stderr.flush()
-    stderr.seek(0)
-    while True:
-        chunk = stderr.read( CHUNK_SIZE )
-        if chunk:
-            stderr_target.write( chunk )
+        os.symlink(options.control_file, os.path.join(tmp_dir, control_filename))
+        cmd = '%s "%s"' % (cmd, control_filename)
+    cmd = '%s "%s" "%s" "%i" "%i" "%i" "%f" "%i" "%s"' % (cmd, tmp_dir, options.dbkey, options.redundancy_threshold, options.window_size, options.fragment_size, options.effective_genome_fraction, options.gap_size, options.error_cut_off)
+
+    # set up stdout and stderr output options
+    stdout = open_file_from_option(options.stdout, mode='wb')
+    with tempfile.NamedTemporaryFile(dir=tmp_dir) as stderr:
+        return_code = subprocess.call(args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir)
+
+        if return_code:
+            try:
+                stderr_target = sys.stderr.buffer
+            except AttributeError:
+                # Python 2
+                stderr_target = sys.stderr
         else:
-            break
-    stderr.close()
-
+            stderr_target = stdout
+            stderr_target.write("\nAdditionally, these warnings were reported:\n")
+        stderr.flush()
+        stderr.seek(0)
+        while True:
+            chunk = stderr.read(CHUNK_SIZE)
+            if chunk:
+                stderr_target.write(chunk)
+            else:
+                break
+    if return_code:
+        cleanup_before_exit(tmp_dir)
+        raise Exception("Error running: %s" % cmd)
+
     try:
-        #move files to where they belong
-        shutil.move(  os.path.join( tmp_dir,'%s-%i-removed.bed' % ( bed_base_filename, options.redundancy_threshold ) ), options.redundancy_removed_test_bed_output_file )
-        shutil.move(  os.path.join( tmp_dir,'%s-W%i.graph' % ( bed_base_filename, options.window_size ) ), options.summary_graph_output_file )
-        if options.fix_off_by_one_errors: add_one_to_file_column( options.summary_graph_output_file, 2 )
-        shutil.move(  os.path.join( tmp_dir,'%s-W%i-normalized.wig' % ( bed_base_filename, options.window_size ) ), options.test_normalized_wig_output_file )
+        # move files to where they belong
+        shutil.move(os.path.join(tmp_dir, '%s-%i-removed.bed' % (bed_base_filename, options.redundancy_threshold)), options.redundancy_removed_test_bed_output_file)
+        shutil.move(os.path.join(tmp_dir, '%s-W%i.graph' % (bed_base_filename, options.window_size)), options.summary_graph_output_file)
+        if options.fix_off_by_one_errors:
+            add_one_to_file_column(options.summary_graph_output_file, 2)
+        shutil.move(os.path.join(tmp_dir, '%s-W%i-normalized.wig' % (bed_base_filename, options.window_size)), options.test_normalized_wig_output_file)
         if options.control_file is not None:
-            shutil.move(  os.path.join( tmp_dir,'%s-%i-removed.bed' % ( control_base_filename, options.redundancy_threshold ) ), options.redundancy_removed_control_bed_output_file )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i.scoreisland' % ( bed_base_filename, options.window_size, options.gap_size ) ), options.score_island_output_file )
-            if options.fix_off_by_one_errors: add_one_to_file_column( options.score_island_output_file, 2 )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-islands-summary' % ( bed_base_filename, options.window_size, options.gap_size ) ), options.islands_summary_output_file )
-            if options.fix_off_by_one_errors: add_one_to_file_column( options.islands_summary_output_file, 2 )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-islands-summary-FDR%s' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.significant_islands_summary_output_file )
-            if options.fix_off_by_one_errors: add_one_to_file_column( options.significant_islands_summary_output_file, 2 )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-FDR%s-island.bed' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.significant_islands_output_file )
-            if options.fix_off_by_one_errors: add_one_to_file_column( options.significant_islands_output_file, 2 )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-FDR%s-islandfiltered.bed' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_output_file )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-FDR%s-islandfiltered-normalized.wig' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_normalized_wig_output_file )
+            shutil.move(os.path.join(tmp_dir, '%s-%i-removed.bed' % (control_base_filename, options.redundancy_threshold)), options.redundancy_removed_control_bed_output_file)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i.scoreisland' % (bed_base_filename, options.window_size, options.gap_size)), options.score_island_output_file)
+            if options.fix_off_by_one_errors:
+                add_one_to_file_column(options.score_island_output_file, 2)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-islands-summary' % (bed_base_filename, options.window_size, options.gap_size)), options.islands_summary_output_file)
+            if options.fix_off_by_one_errors:
+                add_one_to_file_column(options.islands_summary_output_file, 2)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-islands-summary-FDR%s' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.significant_islands_summary_output_file)
+            if options.fix_off_by_one_errors:
+                add_one_to_file_column(options.significant_islands_summary_output_file, 2)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-FDR%s-island.bed' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.significant_islands_output_file)
+            if options.fix_off_by_one_errors:
+                add_one_to_file_column(options.significant_islands_output_file, 2)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-FDR%s-islandfiltered.bed' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.island_filtered_output_file)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-FDR%s-islandfiltered-normalized.wig' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.island_filtered_normalized_wig_output_file)
         else:
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-E%s.scoreisland' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.score_island_output_file )
-            if options.fix_off_by_one_errors: add_one_to_file_column( options.score_island_output_file, 2 )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-E%s-islandfiltered.bed' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_output_file )
-            shutil.move(  os.path.join( tmp_dir,'%s-W%i-G%i-E%s-islandfiltered-normalized.wig' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_normalized_wig_output_file )
-    except Exception, e:
-        raise e
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-E%s.scoreisland' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.score_island_output_file)
+            if options.fix_off_by_one_errors:
+                add_one_to_file_column(options.score_island_output_file, 2)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-E%s-islandfiltered.bed' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.island_filtered_output_file)
+            shutil.move(os.path.join(tmp_dir, '%s-W%i-G%i-E%s-islandfiltered-normalized.wig' % (bed_base_filename, options.window_size, options.gap_size, options.error_cut_off)), options.island_filtered_normalized_wig_output_file)
     finally:
-        cleanup_before_exit( tmp_dir )
+        cleanup_before_exit(tmp_dir)
+

-if __name__=="__main__": __main__()
+if __name__ == "__main__":
+    __main__()
--- a/sicer_wrapper.xml	Wed Oct 24 11:31:03 2018 -0400
+++ b/sicer_wrapper.xml	Wed Oct 28 23:36:25 2020 +0000
@@ -1,155 +1,159 @@
-<tool id="peakcalling_sicer" name="SICER" version="0.0.2">
-  <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
-  <command interpreter="python">sicer_wrapper.py
-  --bed_file '${input_bed_file}'
-  #if str( $input_control_file ) != 'None':
-      --control_file '${input_control_file}'
-      --significant_islands_output_file "${significant_islands_output_file}"
-      --islands_summary_output_file "${islands_summary_output_file}"
-      --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
-  #end if
-  ${fix_off_by_one_errors}
-  --dbkey '${input_bed_file.dbkey}'
-  --redundancy_threshold '${redundancy_threshold}'
-  --window_size '${window_size}'
-  --fragment_size '${fragment_size}'
-  --effective_genome_fraction '${effective_genome_fraction}'
-  --gap_size '${gap_size}'
-  --error_cut_off '${error_cut_off}'
-  ##output files
-  --stdout "${output_log_file}"
-  --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
-  --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
-  --score_island_output_file "${score_island_output_file}"
-  --summary_graph_output_file "${summary_graph_output_file}"
-  --test_normalized_wig_output_file "${test_normalized_wig_output_file}"
-  --island_filtered_output_file "${island_filtered_output_file}"
-  --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
-  </command>
-  <requirements>
-    <requirement type="package" version="1.1">SICER</requirement>
-  </requirements>
-  <inputs>
-    <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
-      <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator>
-    </param>
-    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys -->
-      <options>
-        <filter type="data_meta" ref="input_bed_file" key="dbkey" />
-      </options>
-    </param>
-    <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="True" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/>
-    <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
-    <param name="window_size" type="integer" label="Window size" value="200" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
-    <param name="fragment_size" type="integer" label="Fragment size" value="150" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
-    <param name="effective_genome_fraction" type="float" label="Effective genome fraction" value="0.74" help="Effective Genome as fraction of the genome size. It depends on read length." />
-    <param name="gap_size" type="integer" label="Gap size" value="600" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
-    <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" />
-  </inputs>
-  <outputs>
-    <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
-    <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
-    <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
-    <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
-    <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
-    <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
-    <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
-      <filter>input_control_file is not None</filter>
-    </data>
-    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
-      <param name="input_control_file" />
-      <param name="fix_off_by_one_errors" />
-      <param name="redundancy_threshold" value="1" />
-      <param name="window_size" value="200" />
-      <param name="fragment_size" value="150" />
-      <param name="effective_genome_fraction" value="0.74" />
-      <param name="gap_size" value="600" />
-      <param name="error_cut_off" value="0.01" />
-      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
-      <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
-      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
-      <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
-      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
-      <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
-      <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
-    </test>
-    <test>
-      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
-      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
-      <param name="fix_off_by_one_errors" />
-      <param name="redundancy_threshold" value="1" />
-      <param name="window_size" value="200" />
-      <param name="fragment_size" value="150" />
-      <param name="effective_genome_fraction" value="0.74" />
-      <param name="gap_size" value="600" />
-      <param name="error_cut_off" value="0.01" />
-      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
-      <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
-      <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
-      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
-      <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
-      <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
-      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
-      <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
-      <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
-      <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
-      <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
-    </test>
-    <test>
-      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
-      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
-      <param name="fix_off_by_one_errors" value="True" />
-      <param name="redundancy_threshold" value="1" />
-      <param name="window_size" value="200" />
-      <param name="fragment_size" value="150" />
-      <param name="effective_genome_fraction" value="0.74" />
-      <param name="gap_size" value="600" />
-      <param name="error_cut_off" value="0.01" />
-      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
-      <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
-      <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
-      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
-      <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
-      <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
-      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
-      <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
-      <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
-      <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
-      <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
-    </test>
-    <test>
-      <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
-      <param name="input_control_file" />
-      <param name="fix_off_by_one_errors" value="True" />
-      <param name="redundancy_threshold" value="1" />
-      <param name="window_size" value="200" />
-      <param name="fragment_size" value="150" />
-      <param name="effective_genome_fraction" value="0.74" />
-      <param name="gap_size" value="600" />
-      <param name="error_cut_off" value="0.01" />
-      <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
-      <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
-      <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
-      <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
-      <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
-      <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
-      <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
-    </test>
-  </tests>
-  <help>
+<tool id="peakcalling_sicer" name="SICER" version="@TOOL_VERSION@">
+    <description>Statistical approach for the Identification of ChIP-Enriched Regions</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">SICER</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/sicer_wrapper.py'
+--bed_file '${input_bed_file}'
+#if str($input_control_file) != 'None':
+    --control_file '${input_control_file}'
+    --significant_islands_output_file "${significant_islands_output_file}"
+    --islands_summary_output_file "${islands_summary_output_file}"
+    --significant_islands_summary_output_file "${significant_islands_summary_output_file}"
+#end if
+${fix_off_by_one_errors}
+--dbkey '${input_bed_file.dbkey}'
+--redundancy_threshold '${redundancy_threshold}'
+--window_size '${window_size}'
+--fragment_size '${fragment_size}'
+--effective_genome_fraction '${effective_genome_fraction}'
+--gap_size '${gap_size}'
+--error_cut_off '${error_cut_off}'
+##output files
+--stdout "${output_log_file}"
+--redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}"
+--redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}"
+--score_island_output_file "${score_island_output_file}"
+--summary_graph_output_file "${summary_graph_output_file}"
+--test_normalized_wig_output_file "${test_normalized_wig_output_file}"
+--island_filtered_output_file "${island_filtered_output_file}"
+--island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}"
+    ]]></command>
+    <inputs>
+        <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" >
+            <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in ['mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8']</validator>
+        </param>
+        <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="true"> <!-- fix me, add filter to match dbkeys -->
+            <options>
+                <filter type="data_meta" ref="input_bed_file" key="dbkey" />
+            </options>
+        </param>
+        <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="true" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/>
+        <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" />
+        <param name="window_size" type="integer" value="200" label="Window size" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" />
+        <param name="fragment_size" type="integer" value="150" label="Fragment size" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." />
+        <param name="effective_genome_fraction" type="float" value="0.74" label="Effective genome fraction" help="Effective Genome as fraction of the genome size. It depends on read length." />
+        <param name="gap_size" type="integer" value="600" label="Gap size" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." />
+        <param name="error_cut_off" type="float" value="0.01" label="Statistic threshold value" help="FDR (with control) or E-value (without control)" />
+    </inputs>
+    <outputs>
+        <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/>
+        <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/>
+        <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/>
+        <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/>
+        <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/>
+        <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/>
+        <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})">
+            <filter>input_control_file is not None</filter>
+        </data>
+        <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
+            <param name="input_control_file" />
+            <param name="fix_off_by_one_errors" />
+            <param name="redundancy_threshold" value="1" />
+            <param name="window_size" value="200" />
+            <param name="fragment_size" value="150" />
+            <param name="effective_genome_fraction" value="0.74" />
+            <param name="gap_size" value="600" />
+            <param name="error_cut_off" value="0.01" />
+            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
+            <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
+            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
+            <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
+            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
+            <output name="score_island_output_file" file="test_1_test-W200-G600-E0.01.scoreisland" />
+            <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
+        </test>
+        <test>
+            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
+            <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
+            <param name="fix_off_by_one_errors" />
+            <param name="redundancy_threshold" value="1" />
+            <param name="window_size" value="200" />
+            <param name="fragment_size" value="150" />
+            <param name="effective_genome_fraction" value="0.74" />
+            <param name="gap_size" value="600" />
+            <param name="error_cut_off" value="0.01" />
+            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
+            <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
+            <output name="summary_graph_output_file" file="test_1_test-W200.graph" />
+            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
+            <output name="significant_islands_output_file" file="test_2_test-W200-G600-FDR0.01-island.bed" />
+            <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
+            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
+            <output name="score_island_output_file" file="test_2_test-W200-G600.scoreisland" />
+            <output name="islands_summary_output_file" file="test_2_test-W200-G600-islands-summary" />
+            <output name="significant_islands_summary_output_file" file="test_2_test-W200-G600-islands-summary-FDR0.01" />
+            <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
+        </test>
+        <test>
+            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
+            <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" />
+            <param name="fix_off_by_one_errors" value="True" />
+            <param name="redundancy_threshold" value="1" />
+            <param name="window_size" value="200" />
+            <param name="fragment_size" value="150" />
+            <param name="effective_genome_fraction" value="0.74" />
+            <param name="gap_size" value="600" />
+            <param name="error_cut_off" value="0.01" />
+            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
+            <output name="redundancy_removed_control_bed_output_file" file="control-1-removed.bed" />
+            <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
+            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
+            <output name="significant_islands_output_file" file="test_3_test-W200-G600-FDR0.01-island.bed" />
+            <output name="island_filtered_output_file" file="test-W200-G600-FDR0.01-islandfiltered.bed" />
+            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-FDR0.01-islandfiltered-normalized.wig" />
+            <output name="score_island_output_file" file="test_3_test-W200-G600.scoreisland" />
+            <output name="islands_summary_output_file" file="test_3_test-W200-G600-islands-summary" />
+            <output name="significant_islands_summary_output_file" file="test_3_test-W200-G600-islands-summary-FDR0.01" />
+            <output name="output_log_file" file="test_2_output_log_file.contains" compare="contains"/>
+        </test>
+        <test>
+            <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" />
+            <param name="input_control_file" />
+            <param name="fix_off_by_one_errors" value="True" />
+            <param name="redundancy_threshold" value="1" />
+            <param name="window_size" value="200" />
+            <param name="fragment_size" value="150" />
+            <param name="effective_genome_fraction" value="0.74" />
+            <param name="gap_size" value="600" />
+            <param name="error_cut_off" value="0.01" />
+            <output name="redundancy_removed_test_bed_output_file" file="test-1-removed.bed" />
+            <output name="summary_graph_output_file" file="test_3_test-W200.graph" />
+            <output name="test_normalized_wig_output_file" file="test-W200-normalized.wig" />
+            <output name="island_filtered_output_file" file="test-W200-G600-E0.01-islandfiltered.bed" />
+            <output name="island_filtered_normalized_wig_output_file" file="test-W200-G600-E0.01-islandfiltered-normalized.wig" />
+            <output name="score_island_output_file" file="test_4_test-W200-G600-E0.01.scoreisland" />
+            <output name="output_log_file" file="test_1_output_log_file.contains" compare="contains"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**

 SICER first and foremost is a filtering tool. Its main functions are::
@@ -170,9 +174,8 @@

 **Citation**
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-  </help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btp340</citation>
-  </citations>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp340</citation>
+    </citations>
 </tool>