diff toolfactory/rgToolFactory2.py @ 62:881bd8c81ac9 draft

Uploaded

--- a/toolfactory/rgToolFactory2.py	Thu Oct 22 03:39:09 2020 +0000
+++ b/toolfactory/rgToolFactory2.py	Mon Oct 26 02:51:54 2020 +0000
@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # rgToolFactory.py
 # see https://github.com/fubar2/toolfactory
 #
@@ -325,15 +324,18 @@
         """ no parameters - uses < and > for i/o
         """
         aCL = self.cl.append
-        aCL("<")
-        aCL(self.infiles[0][IPATHPOS])
-        aCL(">")
-        aCL(self.outfiles[0][OCLPOS])
         aXCL = self.xmlcl.append
-        aXCL("<")
-        aXCL("$%s" % self.infiles[0][ICLPOS])
-        aXCL(">")
-        aXCL("$%s" % self.outfiles[0][ONAMEPOS])
+
+        if len(self.infiles) > 0:
+            aCL("<")
+            aCL(self.infiles[0][IPATHPOS])
+            aXCL("<")
+            aXCL("$%s" % self.infiles[0][ICLPOS])
+        if len(self.outfiles) > 0:
+            aCL(">")
+            aCL(self.outfiles[0][OCLPOS])
+            aXCL(">")
+            aXCL("$%s" % self.outfiles[0][ONAMEPOS])
 
     def clpositional(self):
         # inputs in order then params
@@ -482,37 +484,39 @@
 
     def doNoXMLparam(self):
         """filter style package - stdin to stdout"""
-        alab = self.infiles[0][ILABPOS]
-        if len(alab) == 0:
-            alab = self.infiles[0][ICLPOS]
-        max1s = (
-            "Maximum one input if parampass is 0 but multiple input files supplied - %s"
-            % str(self.infiles)
-        )
-        assert len(self.infiles) == 1, max1s
-        newname = self.infiles[0][ICLPOS]
-        aninput = gxtp.DataParam(
-            newname,
-            optional=False,
-            label=alab,
-            help=self.infiles[0][IHELPOS],
-            format=self.infiles[0][IFMTPOS],
-            multiple=False,
-            num_dashes=0,
-        )
-        aninput.command_line_override = "< $%s" % newname
-        aninput.positional = self.is_positional
-        self.tinputs.append(aninput)
-        tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
-        self.testparam.append(tp)
-        newname = self.outfiles[0][OCLPOS]
-        newfmt = self.outfiles[0][OFMTPOS]
-        anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
-        anout.command_line_override = "> $%s" % newname
-        anout.positional = self.is_positional
-        self.toutputs.append(anout)
-        tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt)
-        self.testparam.append(tp)
+        if len(self.infiles) > 0:
+            alab = self.infiles[0][ILABPOS]
+            if len(alab) == 0:
+                alab = self.infiles[0][ICLPOS]
+            max1s = (
+                "Maximum one input if parampass is 0 but multiple input files supplied - %s"
+                % str(self.infiles)
+            )
+            assert len(self.infiles) == 1, max1s
+            newname = self.infiles[0][ICLPOS]
+            aninput = gxtp.DataParam(
+                newname,
+                optional=False,
+                label=alab,
+                help=self.infiles[0][IHELPOS],
+                format=self.infiles[0][IFMTPOS],
+                multiple=False,
+                num_dashes=0,
+            )
+            aninput.command_line_override = "< $%s" % newname
+            aninput.positional = self.is_positional
+            self.tinputs.append(aninput)
+            tp = gxtp.TestParam(name=newname, value="%s_sample" % newname)
+            self.testparam.append(tp)
+        if len(self.outfiles > 0):
+            newname = self.outfiles[0][OCLPOS]
+            newfmt = self.outfiles[0][OFMTPOS]
+            anout = gxtp.OutputData(newname, format=newfmt, num_dashes=0)
+            anout.command_line_override = "> $%s" % newname
+            anout.positional = self.is_positional
+            self.toutputs.append(anout)
+            tp = gxtp.TestOutput(name=newname, value="%s_sample" % newname, format=newfmt)
+            self.testparam.append(tp)
 
     def makeXML(self):
         """
@@ -529,13 +533,13 @@
             safertext = [html_escape(x) for x in helptext]
             if self.args.script_path:
                 scrpt = self.script.split('\n')
-                scrpt.append("```\n")
+                scrpt.insert(0,"```\n")
                 if len(scrpt) > 300:
                     safertext = safertext + scrpt[:100] + ['>500 lines - stuff deleted','......'] + scrpt[-100:]
                 else:
                     safertext = safertext + scrpt
                 safertext.append("\n```")
-            self.newtool.help = "".join([x for x in safertext])
+            self.newtool.help = "\n".join([x for x in safertext])
         else:
             self.newtool.help = (
                 "Please ask the tool author (%s) for help \
@@ -627,8 +631,14 @@
             ste.close()
             retval = p.returncode
         else:  # work around special case - stdin and write to stdout
-            sti = open(self.infiles[0][IPATHPOS], "rb")
-            sto = open(self.outfiles[0][ONAMEPOS], "wb")
+            if len(self.infiles) > 0:
+                sti = open(self.infiles[0][IPATHPOS], "rb")
+            else:
+                sti = sys.stdin    
+            if len(self.outfiles) > 0:
+                sto = open(self.outfiles[0][ONAMEPOS], "wb")
+            else:
+                sto = sys.stdout
             p = subprocess.run(self.cl, shell=False, stdout=sto, stdin=sti)
             retval = p.returncode
             sto.close()
@@ -695,7 +705,6 @@
             cll = [
                 "planemo",
                 "test",
-                "--skip_venv",
                 "--galaxy_root",
                 self.args.galaxy_root,
                 "--update_test_data",
@@ -703,7 +712,7 @@
             ]
         else:
             cll = ["planemo", "test", "--galaxy_root",
-                self.args.galaxy_root, "--skip_venv",
+                self.args.galaxy_root, 
                 xreal,]
         p = subprocess.run(
                 cll, shell=False, cwd=self.tooloutdir, stderr=tout, stdout=tout