Mercurial > repos > iuc > stacks2_sstacks

changeset 6:9586f08634c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
author iuc
date Wed, 11 May 2022 06:51:14 +0000
parents 09b8edb56d80
children a819ec3b362d
files macros.xml stacks_sstacks.xml
diffstat 2 files changed, 9 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 14 09:22:31 2022 +0000
+++ b/macros.xml	Wed May 11 06:51:14 2022 +0000
@@ -10,7 +10,7 @@
     </xml>
 
     <token name="@TOOL_VERSION@">2.55</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.05</token>
 
     <xml name="citation">
@@ -632,4 +632,8 @@
             <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option>
         </expand>
     </xml>
+    <!-- for tests that check the output for "stacks completed" -->
+    <xml name="test_element_stacks_completed" token_element_name="">
+        <element name="@ELEMENT_NAME@"><assert_contents><has_text text="stacks completed on" /></assert_contents></element>
+    </xml>
 </macros>
--- a/stacks_sstacks.xml	Thu Apr 14 09:22:31 2022 +0000
+++ b/stacks_sstacks.xml	Wed May 11 06:51:14 2022 +0000
@@ -114,8 +114,8 @@
             </assert_command>
             <output name="output_log" ftype="txt"><assert_contents><has_text text="done."/></assert_contents></output>
             <output_collection name="matches" type="list" count="2">
-                <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
-                <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.matches" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.matches" />
             </output_collection>
         </test>
 
@@ -149,8 +149,8 @@
             </assert_command>
             <assert_stderr><has_text text="done."/></assert_stderr>
             <output_collection name="matches" type="list" count="2">
-                <element name="PopA_01.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
-                <element name="PopA_02.matches"><assert_contents><has_text text="# sstacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="PopA_01.matches" />
+                <expand macro="test_element_stacks_completed" element_name="PopA_02.matches" />
             </output_collection>
         </test>
     </tests>