diff tools/mummer/mummer.xml @ 6:d9f3d4779507 draft default tip

v0.0.7 stricter error checking; record gnuplot version

--- a/tools/mummer/mummer.xml	Wed Feb 01 06:58:01 2017 -0500
+++ b/tools/mummer/mummer.xml	Wed May 10 12:14:49 2017 -0400
@@ -1,29 +1,18 @@
-<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.6">
+<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.7">
     <description>Combine mummer/nucmer/promer with mummerplot</description>
     <requirements>
             <!-- Needs ps2pdf from ghostscript -->      
-            <requirement type="binary">ps2pdf</requirement>
             <requirement type="package" version="9.10">ghostscript</requirement>
             <!-- Needs mummer, nucmer, promer and mummerplot from MUMmer -->
-            <requirement type="binary">mummer</requirement>
-            <requirement type="binary">nucmer</requirement>
-            <requirement type="binary">promer</requirement>
-            <requirement type="binary">mummerplot</requirement>
             <requirement type="package" version="3.23">mummer</requirement>
 	    <!-- mummerplot needs the gnuplot binary -->
-            <requirement type="binary">gnuplot</requirement>
             <requirement type="package" version="4.6">gnuplot</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">
-mummer.py --version
+    <version_command>
+python $__tool_directory__/mummer.py --version
     </version_command>
-    <command interpreter="python">
-mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output"
+    <command detect_errors="aggressive">
+python $__tool_directory__/mummer.py '$fasta_a' '$fasta_b' $algorithm '$png_output' '$pdf_output'
     </command>
     <inputs>
         <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->