# HG changeset patch
# User peterjc
# Date 1492790871 14400
# Node ID 3dc9fd2ad70cacdbff453afd80a0153dea65a93d
# Parent  6c5822581e417485388c79d6ff6a6aa22afc184d
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty

diff -r 6c5822581e41 -r 3dc9fd2ad70c tools/seq_select_by_id/README.rst
--- a/tools/seq_select_by_id/README.rst	Thu Feb 09 11:28:17 2017 -0500
+++ b/tools/seq_select_by_id/README.rst	Fri Apr 21 12:07:51 2017 -0400
@@ -86,6 +86,8 @@
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
         - Quote filenames in case of spaces (internal change only).
 v0.0.12 - Python style changes (internal change only).
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
 ======= ======================================================================
 
 
diff -r 6c5822581e41 -r 3dc9fd2ad70c tools/seq_select_by_id/seq_select_by_id.xml
--- a/tools/seq_select_by_id/seq_select_by_id.xml	Thu Feb 09 11:28:17 2017 -0500
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Fri Apr 21 12:07:51 2017 -0400
@@ -1,17 +1,13 @@
 <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." />
diff -r 6c5822581e41 -r 3dc9fd2ad70c tools/seq_select_by_id/tool_dependencies.xml
--- a/tools/seq_select_by_id/tool_dependencies.xml	Thu Feb 09 11:28:17 2017 -0500
+++ b/tools/seq_select_by_id/tool_dependencies.xml	Fri Apr 21 12:07:51 2017 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="biopython" version="1.62">
-        <repository changeset_revision="76434ffd927d" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="biopython" version="1.67">
+        <repository changeset_revision="fc45a61abc2f" name="package_biopython_1_67" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>