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changeset 2:0061b5818bb5 draft default tip

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planemo upload for repository https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine commit 059ddaa55a5e4bdac5aaba74fe489e9268731390
author iuc
date Sun, 21 Oct 2018 13:02:43 -0400
parents ee9f908ce860
children
files spotyping.xml
diffstat 1 files changed, 9 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/spotyping.xml	Sat Oct 06 18:48:19 2018 -0400
+++ b/spotyping.xml	Sun Oct 21 13:02:43 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy1" profile="17.01">
+<tool id="spotyping" name="SpoTyping" version="@TOOL_VERSION@+galaxy2" profile="17.01">
   <description>fast and accurate in silico Mycobacterium spoligotyping from sequence reads</description>
 
   <macros>
@@ -9,7 +9,7 @@
     <requirement type="package" version="@TOOL_VERSION@">spotyping</requirement>
   </requirements>
 
-  <command detect_errors="exit_code"><![CDATA[
+  <command detect_errors="aggressive"><![CDATA[
     #set $input_file='input.' + $input.extension
     ln -s '${input}' $input_file &&
     SpoTyping.py
@@ -60,6 +60,13 @@
         </assert_contents>
       </output>
     </test>
+    <test expect_failure="true">
+      <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
+      <param name="seq" value="--seq" />
+      <assert_stderr>
+        <has_text text="BLAST options error" />
+      </assert_stderr>
+    </test>
     <test expect_num_outputs="2">
       <param name="input" value="input.fastq.gz" ftype="fastq.gz" />
       <param name="noQuery" value="" />