bcsplitter fix missing when (#6430)

galaxyproject · Oct 5, 2024 · 9be97b7 · 9be97b7
1 parent ff1576c
commit 9be97b7
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Showing 2 changed files with 14 additions and 12 deletions.
diff --git a/tools/barcode_splitter/.lint_skip b/tools/barcode_splitter/.lint_skip
diff --git a/tools/barcode_splitter/barcode_splitter.xml b/tools/barcode_splitter/barcode_splitter.xml
@@ -276,20 +276,24 @@
                                 </sanitizer>
                             </param>
                         </when>
-                        <when value="singleindex">
+                        <when value="forward"/>
+                        <when value="reverse"/>
+                        <when value="index">
                             <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc..  Ignored for paired-collections.  Letters and numbers only.  No spaces.  Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">
                                 <sanitizer>
                                     <valid initial="string.ascii_letters,string.digits" />
                                 </sanitizer>
                             </param>
                         </when>
-                        <when value="index">
+                        <when value="singleindex">
                             <param name="readname" type="text" label="Read Name" help="E.g. index1, index2, etc..  Ignored for paired-collections.  Letters and numbers only.  No spaces.  Default is 'read-x' where 'x' is a number corresponding to the order in which the file was supplied.">
                                 <sanitizer>
                                     <valid initial="string.ascii_letters,string.digits" />
                                 </sanitizer>
                             </param>
                         </when>
+                        <when value="forwardindex"/>
+                        <when value="reverseindex"/>
                     </conditional>
                 </repeat>
             </when>
@@ -335,7 +339,7 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <!-- single end with 1 index -->
             <param name="run_type" value="single" />
             <param name="bcfile" value="barcode_splitter_barcodes.txt" />
@@ -359,7 +363,7 @@
                 <element name="multimatched" ftype="fastq" file="test_1_multimatched-read-1.out" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <!-- single end with 1 index and split all -->
             <param name="run_type" value="single" />
             <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />
@@ -401,7 +405,7 @@
                 <element name="multimatched index2" ftype="fastq" file="test_2_multimatched_index2.fastq" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- paired end with one index -->
             <param name="run_type" value="paired" />
             <param name="bcfile" value="barcode_splitter_barcodes.txt" />
@@ -444,7 +448,7 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <!-- paired end 2 indexes and split_all -->
             <param name="run_type" value="paired" />
             <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />
@@ -505,7 +509,7 @@
                 <element name="multimatched index2" ftype="fastq" file="test_2_multimatched_index2.fastq" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- flexible with single end containing index -->
             <param name="bcfile" value="barcode_splitter_barcodes.txt" />
             <param name="mismatches" value="2" />
@@ -533,7 +537,7 @@
                 <element name="multimatched" ftype="fastq" file="test_1_multimatched-read-1.out" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <!-- flexible with first single end no index, second containing index, 1 separate index, and split all -->
             <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />
             <param name="mismatches" value="2" />
@@ -589,7 +593,7 @@
                 <element name="multimatched index2" ftype="fastq" file="test_6_multimatched_index2.fastq" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <!-- flexible with paired end with one index and no split all -->
             <param name="bcfile" value="barcode_splitter_barcodes.txt" />
             <param name="mismatches" value="2" />
@@ -649,7 +653,7 @@
                 </element>
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <!-- flexible with paired end with reverseindex, single end, separate index, and no split all -->
             <param name="bcfile" value="barcode_splitter_barcodes_dual.txt" />
             <param name="mismatches" value="2" />