Mercurial > repos > iuc > stacks2_cstacks

changeset 6:8501601a118d 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 06:44:59 +0000
parents 0cd2df8af811
children 42d9087b4789
files macros.xml stacks_cstacks.xml
diffstat 2 files changed, 11 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 14 09:24:41 2022 +0000
+++ b/macros.xml	Wed May 11 06:44:59 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_cstacks.xml	Thu Apr 14 09:24:41 2022 +0000
+++ b/stacks_cstacks.xml	Wed May 11 06:44:59 2022 +0000
@@ -110,9 +110,9 @@
             <param name="add_log" value="yes"/>
             <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
             <output_collection name="catalog" type="list">
-                <element name="catalog.alleles"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
-                <element name="catalog.snps"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
-                <element name="catalog.tags"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="catalog.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="catalog.snps" />
+                <expand macro="test_element_stacks_completed" element_name="catalog.tags" />
             </output_collection>
         </test>
         <!-- test w non default options (wo gapped, because tested already in ustacks) -->
@@ -139,9 +139,9 @@
             <param name="add_log" value="no"/>
             <assert_stderr><has_text text="done."/></assert_stderr>
             <output_collection name="catalog" type="list">
-                <element name="catalog.alleles"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
-                <element name="catalog.snps"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
-                <element name="catalog.tags"><assert_contents><has_text text="# cstacks completed on "/></assert_contents></element>
+                <expand macro="test_element_stacks_completed" element_name="catalog.alleles" />
+                <expand macro="test_element_stacks_completed" element_name="catalog.snps" />
+                <expand macro="test_element_stacks_completed" element_name="catalog.tags" />
             </output_collection>
         </test>
     </tests>