changeset 11:566e42c97532

Uploaded tarball. Testing automated tests.

--- a/allele-counts.xml	Fri Sep 06 20:37:07 2013 -0400
+++ b/allele-counts.xml	Tue Sep 10 13:00:28 2013 -0400
@@ -1,13 +1,14 @@
 <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</command>
+  <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt -r $seed</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 (in percent)"/>
-    <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (in reads per strand)"/>
+    <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="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"/>
@@ -17,6 +18,16 @@
     <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

--- a/tests/run-tests.py	Fri Sep 06 20:37:07 2013 -0400
+++ b/tests/run-tests.py	Tue Sep 10 13:00:28 2013 -0400
@@ -16,12 +16,49 @@
 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
@@ -34,11 +71,48 @@
       continue
 
     options = read_options(infile)
-    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])
+    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')
 
 
 def read_options(infile):