# HG changeset patch
# User nick
# Date 1378833247 14400
# Node ID 97b772e3a0f10a3076cf216c8f94e8f5c7b7ce58
# Parent  566e42c97532b12b736827552d2fbc9f502eb4b8
Uploaded tarball.

diff -r 566e42c97532 -r 97b772e3a0f1 allele-counts.xml
--- a/allele-counts.xml	Tue Sep 10 13:00:28 2013 -0400
+++ b/allele-counts.xml	Tue Sep 10 13:14:07 2013 -0400
@@ -1,14 +1,13 @@
 <tool id="allele_counts_1" version="1.1" name="Variant Annotator">
   <description> process variant counts</description>
-  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt -r $seed</command>
+  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt</command>
   <inputs>
     <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
-    <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/>
-    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/>
+    <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold (in percent)"/>
+    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (in reads per strand)"/>
     <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" />
     <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" />
     <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" />
-    <param name="seed" type="text" value="" label="PRNG seed" />
   </inputs>
   <outputs>
     <data name="output" format="tabular"/>
@@ -18,16 +17,6 @@
     <exit_code range=":-1" err_level="fatal"/>
   </stdio>
 
-  <tests>
-    <test>
-      <param name="input" value="tests/artificial.vcf.in" />
-      <param name="freq" value="10" />
-      <param name="covg" value="10" />
-      <param name="seed" value="1" />
-      <output name="output" file="tests/artificial.csv.out" />
-    </test>
-  </tests>
-
   <help>
 
 .. class:: infomark
diff -r 566e42c97532 -r 97b772e3a0f1 tests/run-tests.py
--- a/tests/run-tests.py	Tue Sep 10 13:00:28 2013 -0400
+++ b/tests/run-tests.py	Tue Sep 10 13:14:07 2013 -0400
@@ -16,49 +16,12 @@
 OUT_EXT = '.csv.out'
 ARGS_KEY = '##comment="ARGS='
 
-XML = {
-  'tests_start':'  <tests>',
-  'test_start': '    <test>',
-  'input':      '      <param name="input" value="tests/%s" />',
-  'param':      '      <param name="%s" value="%s" />',
-  'output':     '      <output name="output" file="tests/%s" />',
-  'test_end':   '    </test>',
-  'tests_end':  '  </tests>',
-}
-PARAMS = {
-  '-f':'freq',
-  '-c':'covg',
-  '-H':'header',
-  '-s':'stranded',
-  '-n':'nofilt',
-  '-r':'seed',
-}
-PARAM_ARG = {
-  '-f':True,
-  '-c':True,
-  '-H':False,
-  '-s':False,
-  '-n':False,
-  '-r':True,
-}
-
 def main():
 
-  do_print_xml = False
-  if len(sys.argv) > 1:
-    if sys.argv[1] == '-x':
-      do_print_xml = True
-    else:
-      sys.stderr.write("Error: unrecognized option '"+sys.argv[1]+"'\n")
-      sys.exit(1)
-
   test_dir = os.path.dirname(os.path.relpath(sys.argv[0]))
   if test_dir:
     test_dir += os.sep
 
-  if do_print_xml:
-    print XML.get('tests_start')
-
   for dataset in DATASETS:
     infile  = test_dir+dataset+IN_EXT
     outfile = test_dir+dataset+OUT_EXT
@@ -71,48 +34,11 @@
       continue
 
     options = read_options(infile)
-    if do_print_xml:
-      print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG)
-    else:
-      run_tests(infile, outfile, options)
-
-  if do_print_xml:
-    print XML.get('tests_end')
-
-
-def run_tests(infile, outfile, options):
-  script_cmd = 'allele-counts.py '+options+' -i '+infile
-  bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
-  print script_cmd
-  subprocess.call(['bash', '-c', bash_cmd])
-
-
-def print_xml(infile, outfile, options_str, xml, params, param_arg):
-  infile = os.path.basename(infile)
-  outfile = os.path.basename(outfile)
-
-  options = options_str.split()  # on whitespace
-
-  print xml.get('test_start')
-  print xml.get('input') % infile
-
-  i = 0
-  while i < len(options):
-    opt = options[i]
-    if not params.has_key(opt) or not param_arg.has_key(opt):
-      sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "
-        +infile+"\n")
-      sys.exit(1)
-    if param_arg[opt]:
-      i+=1
-      arg = options[i]
-      print xml.get('param') % (params[opt], arg)
-    else:
-      print xml.get('param') % (params[opt], opt)
-    i+=1
-
-  print xml.get('output') % outfile
-  print xml.get('test_end')
+    script_cmd = 'allele-counts.py '+options+' -i '+infile
+    bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
+    # print infile+":"
+    print script_cmd
+    subprocess.call(['bash', '-c', bash_cmd])
 
 
 def read_options(infile):