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changeset 12:caf5b859cf7b draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty
author peterjc
date Fri, 21 Apr 2017 12:03:10 -0400
parents b6a958276ef7
children 0b38302b09c7
files tools/mummer/README.rst tools/mummer/mummer.xml
diffstat 2 files changed, 7 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/tools/mummer/README.rst	Thu Feb 09 11:23:58 2017 -0500
+++ b/tools/mummer/README.rst	Fri Apr 21 12:03:10 2017 -0400
@@ -67,6 +67,8 @@
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 v0.0.6  - PEP8 style changes to Python script (internal change only).
         - Fixed display of input parameter help text.
+v0.0.7  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
--- a/tools/mummer/mummer.xml	Thu Feb 09 11:23:58 2017 -0500
+++ b/tools/mummer/mummer.xml	Fri Apr 21 12:03:10 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 -->