# HG changeset patch
# User peterjc
# Date 1494521007 14400
# Node ID 7a05cb080ea5b4df5c271330b1f28907611806ad
# Parent  4200518b0febc43d82643c561b94ea28a5899c85
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants commit 2c1cc3ac829140d469816ec5e9892f96624270bf-dirty

diff -r 4200518b0feb -r 7a05cb080ea5 tools/count_roi_variants/README.rst
--- a/tools/count_roi_variants/README.rst	Thu May 11 10:05:08 2017 -0400
+++ b/tools/count_roi_variants/README.rst	Thu May 11 12:43:27 2017 -0400
@@ -80,6 +80,9 @@
 v0.0.2  - Cope with pipes in reference name (e.g. NCBI style FASTA naming)
 v0.0.3  - Include a functional test for using an unrecognised reference.
 v0.0.4  - Improved usage text and README for use outside of Galaxy.
+v0.0.5  - Fix samtools dependency version inconsistency, using v1.2 now.
+        - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
diff -r 4200518b0feb -r 7a05cb080ea5 tools/count_roi_variants/count_roi_variants.xml
--- a/tools/count_roi_variants/count_roi_variants.xml	Thu May 11 10:05:08 2017 -0400
+++ b/tools/count_roi_variants/count_roi_variants.xml	Thu May 11 12:43:27 2017 -0400
@@ -1,15 +1,14 @@
-<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.3">
+<tool id="count_roi_variants" name="Count sequence variants in region of interest" version="0.0.5">
     <description>using samtools view</description>
     <requirements>
-        <requirement type="package" version="1.2.2">samtools</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">count_roi_variants.py --version</version_command>
-    <command interpreter="python">count_roi_variants.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular" "$region"</command>
+    <version_command>
+python $__tool_directory__/count_roi_variants.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/count_roi_variants.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular' '$region'
+    </command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Input BAM file" />
         <param name="region" type="text" label="Region of interest" help="Use the reference:start-end syntax as in samtools.">