change the test such that files will be compared

galaxyproject · Jul 23, 2024 · 855fae6 · 855fae6
1 parent d3876fb
commit 855fae6
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Showing 4 changed files with 14 additions and 20 deletions.
diff --git a/tools/taxonkit/taxonkit_name2taxid.xml b/tools/taxonkit/taxonkit_name2taxid.xml
@@ -67,12 +67,7 @@
 				<param name="is_select" value="dm"/> 
 				<param name="ncbi" value="test-db-tox" />
 			</conditional>
-            <output name="output">
-                <assert_contents>
-                    <has_text text="9606" n="1"/>
-                    <has_text text="349741" n="1"/>
-                </assert_contents>
-            </output>
+            <output name="output" file="name2taxid_result1.tsv"/>
         </test>
         <test>
             <param name="input" value="name2taxid_test2.tsv" ftype="tabular" />
@@ -81,14 +76,7 @@
 				<param name="ncbi" value="test-db-tox" />
 			</conditional>
 			<param name="name_field" value="2" />
-			<output name="output">
-                <assert_contents>
-                    <has_text text="test" n="4"/>
-					<has_text text="Akkermansia muciniphila ATCC BAA-835" n="1"/>
-					<has_text text="Akkermansia muciniphila" n="2"/>
-					<has_text text="349741" n="1"/>
-				</assert_contents>
-			</output>
+			<output name="output" file="name2taxid_result2.tsv"/>
 		</test>
 		<test>
 			<param name="input" value="name2taxid_test3.txt" ftype="tabular"/>
@@ -99,12 +87,7 @@
 			</conditional>
 			<param name="sci_name" value="true"/>
 			<param name="show_rank" value="true"/>
-			<output name="output">
-				<assert_contents>
-					<has_text text="Drosophila" n="3"/>
-					<has_text text="32281" n="1"/>
-				</assert_contents>
-			</output>
+			<output name="output" file="name2taxid_result3.tsv"/>
 		</test>
     </tests>
     <help>

diff --git a/tools/taxonkit/test-data/name2taxid_result1.tsv b/tools/taxonkit/test-data/name2taxid_result1.tsv
@@ -0,0 +1,4 @@
+Homo sapiens	9606
+Akkermansia muciniphila ATCC BAA-835	349741
+Akkermansia muciniphila	239935
+Mouse Intracisternal A-particle	11932
diff --git a/tools/taxonkit/test-data/name2taxid_result2.tsv b/tools/taxonkit/test-data/name2taxid_result2.tsv
@@ -0,0 +1,4 @@
+test	Homo sapiens	9606
+test	Akkermansia muciniphila ATCC BAA-835	349741
+test	Akkermansia muciniphila	239935
+test	Mouse Intracisternal A-particle	11932
diff --git a/tools/taxonkit/test-data/name2taxid_result3.tsv b/tools/taxonkit/test-data/name2taxid_result3.tsv
@@ -0,0 +1,3 @@
+Drosophila	7215	
+Drosophila	32281	
+Drosophila	2081351