diff rgToolFactory.py @ 13:7725e4ab27e1

Adding tests - problem to find the script - needs a fixed string somewhere. Updated readme

--- a/rgToolFactory.py	Sun Jun 03 15:39:20 2012 +1000
+++ b/rgToolFactory.py	Sun Jun 03 22:25:46 2012 +1000
@@ -93,7 +93,52 @@
     def makeXML(self):
         """
         Create a Galaxy xml tool wrapper for the new script as a string to write out
-        fixme - use templating or something less fugly than this
+        fixme - use templating or something less fugly than this.
+        Here's an example of what we produce
+
+        <tool id="reverse" name="reverse" version="0.01">
+            <description>a tabular file</description>
+            <command interpreter="python">
+            reverse.py --script_path "$runMe" --interpreter "python" 
+            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" 
+            </command>
+            <inputs>
+            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
+
+            </inputs>
+            <outputs>
+            <data format="tabular" name="tab_file" label="${job_name}"/>
+
+            </outputs>
+            <help>
+            
+**What it Does**
+
+Reverse the columns in a tabular file
+
+            </help>
+            <configfiles>
+            <configfile name="runMe">
+            
+# reverse order of columns in a tabular file
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r')
+o = open(outp,'w')
+for row in i:
+     rs = row.rstrip().split('\t')
+     rs.reverse()
+     o.write('\t'.join(rs))
+     o.write('\n')
+i.close()
+o.close()
+ 
+
+            </configfile>
+            </configfiles>
+            </tool>
+        
         """    
         newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="0.01">
             %(tooldesc)s
@@ -112,13 +157,18 @@
             %(script)s
             </configfile>
             </configfiles>
+            %(tooltests)s
             </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
                
         newCommand="""<command interpreter="python">
             %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
             --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
             </command>""" # may NOT be an input or htmlout
-            
+        tooltests = """<tests><test>
+        <param name="input1" value="%s" ftype="%s"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        </test><tests>"""
         xdict = {}
         xdict['script'] = self.script # configfile is least painful way to embed script to avoid external dependencies
         if self.opts.help_text: