diff tools/seq_filter_by_id/seq_filter_by_id.xml @ 9:141612f8c3e3 draft

v0.2.7 Python 3 compatible print etc

--- a/tools/seq_filter_by_id/seq_filter_by_id.xml	Wed May 10 13:18:01 2017 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml	Thu May 11 12:18:52 2017 -0400
@@ -1,22 +1,19 @@
-<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.6">
+<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.7">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">seq_filter_by_id.py --version</version_command>
-    <command interpreter="python">
-seq_filter_by_id.py -i "$input_file" -f "$input_file.ext"
+    <version_command>
+python $__tool_directory__/seq_filter_by_id.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_filter_by_id.py -i '$input_file' -f '$input_file.ext'
 #if str($output_choice_cond.output_choice)=="both"
- -p "$output_pos" -n "$output_neg"
+ -p '$output_pos' -n '$output_neg'
 #elif str($output_choice_cond.output_choice)=="pos"
- -p "$output_pos"
+ -p '$output_pos'
 #elif str($output_choice_cond.output_choice)=="neg"
- -n "$output_neg"
+ -n '$output_neg'
 #end if
 #if str($adv_opts.adv_opts_selector)=="advanced" and $adv_opts.strip_suffix
  -s
@@ -24,9 +21,9 @@
 #if str($id_opts.id_opts_selector)=="tabular":
 ## TODO - Decide on best way to expose multiple ID files via the XML wrapper.
 ## Single tabular file, can call the Python script with either UNION or INTERSECTION
--l UNION "$id_opts.input_tabular" "$id_opts.columns"
+-l UNION '$id_opts.input_tabular' '$id_opts.columns'
 #else
--t "$id_opts.id_list"
+-t '$id_opts.id_list'
 #end if
     </command>
     <inputs>