# HG changeset patch
# User peterjc
# Date 1492790794 14400
# Node ID c64494ea41ea8171d35833f1fb2298e0209d3756
# Parent  69decf35d578396f5ed250f86fa5bb3c796dda99
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping commit 6d77d2fbb0d3ea1fd4db369073654b8a920c44bf-dirty

diff -r 69decf35d578 -r c64494ea41ea tools/seq_filter_by_mapping/README.rst
--- a/tools/seq_filter_by_mapping/README.rst	Thu Feb 09 11:27:06 2017 -0500
+++ b/tools/seq_filter_by_mapping/README.rst	Fri Apr 21 12:06:34 2017 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to filter FASTA, FASTQ or SFF sequences by SAM/BAM mapping
 ======================================================================
 
-This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute
+This tool is copyright 2014-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -67,6 +67,9 @@
         - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 v0.0.5  - Python script cleanups (internal change only).
+        - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r 69decf35d578 -r c64494ea41ea tools/seq_filter_by_mapping/seq_filter_by_mapping.xml
--- a/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml	Thu Feb 09 11:27:06 2017 -0500
+++ b/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml	Fri Apr 21 12:06:34 2017 -0400
@@ -1,28 +1,23 @@
 <tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.5">
     <description>from SAM/BAM file</description>
     <requirements>
-        <requirement type="package" version="1.64">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
-        <requirement type="binary">samtools</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
         <requirement type="package" version="0.1.19">samtools</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_mapping.py --version</version_command>
-    <command interpreter="python">
-seq_filter_by_mapping.py -i "$input_file" -f "$input_file.ext" -m $pair_mode
+    <version_command>
+python $__tool_directory__/seq_filter_by_mapping.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/seq_filter_by_mapping.py -i '$input_file' -f '$input_file.ext' -m $pair_mode
 #if $output_choice_cond.output_choice=="both"
- -p $output_pos -n $output_neg
+ -p '$output_pos' -n '$output_neg'
 #elif $output_choice_cond.output_choice=="pos"
- -p $output_pos
+ -p '$output_pos'
 #elif $output_choice_cond.output_choice=="neg"
- -n $output_neg
+ -n '$output_neg'
 #end if
 ## Now loop over all the mapping files
-#for i in $mapping_file#${i} #end for#
+#for i in $mapping_file#'${i}' #end for#
     </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
diff -r 69decf35d578 -r c64494ea41ea tools/seq_filter_by_mapping/tool_dependencies.xml
--- a/tools/seq_filter_by_mapping/tool_dependencies.xml	Thu Feb 09 11:27:06 2017 -0500
+++ b/tools/seq_filter_by_mapping/tool_dependencies.xml	Fri Apr 21 12:06:34 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="biopython" version="1.64">
-        <repository changeset_revision="bc1d7fa4ad08" name="package_biopython_1_64" 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>
     <package name="samtools" version="0.1.19">
         <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />