diff tools/samtools_idxstats/samtools_idxstats.xml @ 2:71afa65f444a draft default tip

v0.0.5 Internal changes to command line handling

--- a/tools/samtools_idxstats/samtools_idxstats.xml	Wed May 13 10:35:50 2015 -0400
+++ b/tools/samtools_idxstats/samtools_idxstats.xml	Tue May 16 09:24:18 2017 -0400
@@ -1,16 +1,14 @@
-<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4">
+<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.5">
     <description>samtools idxstats</description>
     <requirements>
-        <requirement type="binary">samtools</requirement>
         <requirement type="package" version="0.1.19">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">samtools_idxstats.py --version</version_command>
-    <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
+    <version_command>
+python $__tool_directory__/samtools_idxstats.py --version
+    </version_command>
+    <command  detect_errors="aggressive">
+python $__tool_directory__/samtools_idxstats.py '$input_bam' '${input_bam.metadata.bam_index}' '$out_tabular'
+    </command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Input BAM file" />
     </inputs>