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diff fastq_trimmer.xml @ 7:fe86fb89562d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:51:05 +0000
parents f0b18efb97f1
children
line wrap: on
line diff
--- a/fastq_trimmer.xml	Fri Oct 04 10:35:28 2024 +0000
+++ b/fastq_trimmer.xml	Sun Nov 23 17:51:05 2025 +0000
@@ -38,44 +38,54 @@
         <test>
             <!-- Do nothing trim -->
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="0"/>
-            <param name="right_column_offset" value="0"/>
-            <param name="keep_zero_length" value="keep_zero_length" />
+            <conditional name="offset_type">
+                <param name="base_offset_type" value="offsets_absolute"/>
+                <param name="left_column_offset" value="0"/>
+                <param name="right_column_offset" value="0"/>
+            </conditional>
+            <param name="keep_zero_length" value="true" />
             <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
         </test>
         <!-- Trim to empty File -->
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="30"/>
-            <param name="right_column_offset" value="64"/>
-            <param name="keep_zero_length" value="exclude_zero_length" />
+            <conditional name="offset_type">
+                <param name="base_offset_type" value="offsets_absolute"/>
+                <param name="left_column_offset" value="30"/>
+                <param name="right_column_offset" value="64"/>
+            </conditional>
+            <param name="keep_zero_length" value="false" />
             <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="base_offset_type" value="offsets_percent"/>
-            <param name="left_column_offset" value="50"/>
-            <param name="right_column_offset" value="50"/>
-            <param name="keep_zero_length" value="exclude_zero_length" />
+            <conditional name="offset_type">
+                <param name="base_offset_type" value="offsets_percent"/>
+                <param name="left_column_offset" value="50"/>
+                <param name="right_column_offset" value="50"/>
+            </conditional>
+            <param name="keep_zero_length" value="false" />
             <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
         </test>
         <!-- Trim to 4 inner-most bases -->
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="base_offset_type" value="offsets_absolute"/>
-            <param name="left_column_offset" value="45"/>
-            <param name="right_column_offset" value="45"/>
-            <param name="keep_zero_length" value="exclude_zero_length" />
+            <conditional name="offset_type">
+                <param name="base_offset_type" value="offsets_absolute"/>
+                <param name="left_column_offset" value="45"/>
+                <param name="right_column_offset" value="45"/>            
+            </conditional>
+            <param name="keep_zero_length" value="false" />
             <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
         </test>
         <test>
             <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
-            <param name="base_offset_type" value="offsets_percent"/>
-            <param name="left_column_offset" value="47.87"/>
-            <param name="right_column_offset" value="47.87"/>
-            <param name="keep_zero_length" value="exclude_zero_length" />
+            <conditional name="offset_type">
+                <param name="base_offset_type" value="offsets_percent"/>
+                <param name="left_column_offset" value="47.87"/>
+                <param name="right_column_offset" value="47.87"/>
+            </conditional>
+            <param name="keep_zero_length" value="false" />
             <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
         </test>
     </tests>