Mercurial > repos > peterjc > fastq_paired_unpaired

changeset 7:2709a0f065c9 draft

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v0.1.4 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 08:53:57 -0400
parents f396701fbf32
children 8cbc866b72ce
files tools/fastq_paired_unpaired/README.rst tools/fastq_paired_unpaired/fastq_paired_unpaired.xml
diffstat 2 files changed, 10 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/tools/fastq_paired_unpaired/README.rst	Wed May 10 13:28:59 2017 -0400
+++ b/tools/fastq_paired_unpaired/README.rst	Tue May 16 08:53:57 2017 -0400
@@ -74,6 +74,8 @@
 v0.1.3  - Minor internal changes to Python script for error reporting & style.
         - Updated to point at Biopython 1.67 (latest version in Tool Shed).
         - Explicit dependency on ``galaxy_sequence_utils``.
+v0.1.4  - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
 ======= ======================================================================
 
 
--- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml	Wed May 10 13:28:59 2017 -0400
+++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml	Tue May 16 08:53:57 2017 -0400
@@ -1,21 +1,18 @@
-<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.3">
+<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4">
     <description>using the read name suffices</description>
     <requirements>
         <requirement type="package" version="1.0.1">galaxy_sequence_utils</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">fastq_paired_unpaired.py --version</version_command>
-    <command interpreter="python">
-fastq_paired_unpaired.py $input_fastq.extension $input_fastq
+    <version_command>
+python $__tool_directory__/fastq_paired_unpaired.py --version
+    </version_command>
+    <command detect_errors="aggressive">
+python $__tool_directory__/fastq_paired_unpaired.py '$input_fastq.extension' '$input_fastq'
 #if $output_choice_cond.output_choice=="separate"
- $output_forward $output_reverse
+ '$output_forward' '$output_reverse'
 #elif $output_choice_cond.output_choice=="interleaved"
- $output_paired
+ '$output_paired'
 #end if
 $output_singles
     </command>