diff tools/seq_select_by_id/seq_select_by_id.xml @ 7:a5602454b0ad draft

v0.0.12 Depends on Biopython 1.67 via legacy Tool Shed package or bioconda; Python 3 compatible print function

--- a/tools/seq_select_by_id/seq_select_by_id.xml	Wed May 13 10:56:29 2015 -0400
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Thu May 11 06:26:05 2017 -0400
@@ -1,17 +1,13 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11">
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.12">
     <description>from a tabular file</description>
     <requirements>
-        <requirement type="package" version="1.62">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
+        <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_select_by_id.py --version</version_command>
-    <command interpreter="python">
-seq_select_by_id.py "$input_tabular" "$column" "$input_file" "$input_file.ext" "$output_file"
+    <version_command>
+python $__tool_directory__/seq_select_by_id.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_select_by_id.py '$input_tabular' '$column' '$input_file' '$input_file.ext' '$output_file'
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." />