--- a/bedClean.py	Sat Mar 31 13:03:54 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-import sys
-
-def readChrSize(filename):
-    f = open(filename)
-    chrSize = {}
-    for line in f:
-        chrom,size = line.strip().split()
-        chrSize[chrom]=int(size)
-    f.close()
-    return chrSize
-
-def cleanFile(filename,chrSize,outfile):
-    f = open(filename)
-    out = open(outfile,'w')
-    i = 0
-    for line in f:
-        i = i + 1
-        flds = line.strip().split('\t')
-        if len(flds) < 3:
-            print 'line',i,'incomplete line:\n',line
-        elif chrSize.has_key(flds[0]):
-            if int(flds[1]) > int(flds[2]):
-                tmp = flds[1]
-                flds[1] = flds[2]
-                flds[2] = tmp
-            if int( flds[1]) < 0 or int(flds[2]) <0:
-                print 'line',i,'negative coordinates:\n',line
-            elif int(flds[2]) > chrSize[flds[0]]:
-                print 'line',i,'end larger than chr size:\n',line
-            else:
-                if flds[5] == '*':
-                    flds[5] = '+'
-                    print 'line',i,' strand * changed to +\n', line
-                out.write('\t'.join(flds)+'\n')
-        else:
-            print 'line',i,'chromosome',flds[0],'not found!\n',line
-    f.close()
-    out.close()
-
-if len(sys.argv) < 4:
-    print "python bedClean.py in.bed chrsizefile out.bed"
-    exit()
-cleanFile(sys.argv[1],readChrSize(sys.argv[2]),sys.argv[3])

--- a/bedclean.xml	Sat Mar 31 13:03:54 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<tool id="bedclean" name="clean interval">
-  <description>remove off-chromosome lines</description>
-  <command interpreter="python">bedclean.py $input $genome $output > $log  </command>
-  <inputs>
-     <param name="input" type="data" format="interval" label="Original interval file"/>
-
-            <param name="genome" type="select" label="Select chromsome size file" >
-                <options from_file="chrsize.loc">
-                    <column name="name" index="0"/>
-                    <column name="value" index="1"/>
-                </options>
-            </param>
-
-  </inputs>
-  <outputs>
-    <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
-    <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
-  </outputs>
-  <help>
-
-**Description**
-
-remove lines that are
-
-1. comment or track name lines
-
-2. on chr*_random
-
-3. or have negative coordinates
-
-4. or the end is larger than chromosome size
-
-
-  </help>
-</tool>