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changeset 6:2f901e9402dd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_phase commit 8d2369dc1bdafc743920a155c508c20114ebe655
author iuc
date Mon, 17 Nov 2025 07:30:45 +0000
parents b85b9712cb18
children
files samtools_phase.xml
diffstat 1 files changed, 36 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_phase.xml	Wed Nov 12 13:04:22 2025 +0000
+++ b/samtools_phase.xml	Mon Nov 17 07:30:45 2025 +0000
@@ -48,41 +48,62 @@
         <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
     </outputs>
     <tests>
+        <!-- 1) -->
         <test>
-            <param name="option_sets" value="default" />
+            <conditional name="option_set">
+                <param name="option_sets" value="default" />
+            </conditional>
             <param name="input_bam" value="samtools_phase_in_1.bam" />
-            <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
-            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" lines_diff="4" />
-            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" lines_diff="4" />
-            <output name="chimera" file="empty_file_1.bam" ftype="bam" lines_diff="4" />
+            <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression="Descriptions:"/>
+                </assert_contents>
+            </output>
+            <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" compare="sim_size"/>
+            <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" compare="sim_size"/>
+            <output name="chimera" file="empty_file_1.bam" ftype="bam" compare="sim_size"/>
         </test>
+        <!-- 2) -->
         <test>
             <param name="input_bam" value="samtools_phase_in_2.bam" />
-            <param name="option_sets" value="advanced" />
+            <conditional name="option_set">
+                <param name="option_sets" value="advanced" />
+            </conditional>
             <param name="option_set|block_length" value="13" />
             <param name="option_set|min_het" value="37" />
             <param name="option_set|min_bq" value="13" />
             <param name="option_set|read_depth" value="256" />
             <param name="option_set|ignore_chimeras" value="false" />
             <param name="option_set|drop_ambiguous" value="true" />
-            <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
-            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" lines_diff="4" />
-            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" lines_diff="4" />
-            <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" lines_diff="4" />
+            <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression="Descriptions:"/>
+                </assert_contents>
+            </output>
+            <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" compare="sim_size"/>
+            <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" compare="sim_size"/>
+            <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" compare="sim_size"/>
         </test>
+        <!-- 3) -->
         <test>
             <param name="input_bam" value="samtools_phase_in_2.bam" />
-            <param name="option_sets" value="advanced" />
+            <conditional name="option_set">
+                <param name="option_sets" value="advanced" />
+            </conditional>
             <param name="option_set|block_length" value="13" />
             <param name="option_set|min_het" value="37" />
             <param name="option_set|min_bq" value="13" />
             <param name="option_set|read_depth" value="256" />
             <param name="option_set|ignore_chimeras" value="true" />
             <param name="option_set|drop_ambiguous" value="false" />
-            <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
-            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" lines_diff="4" />
-            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" lines_diff="4" />
-            <output name="chimera" file="empty_file_3.bam" ftype="bam" lines_diff="4" />
+            <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression="Descriptions:"/>
+                </assert_contents>
+            </output>
+            <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" compare="sim_size"/>
+            <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" compare="sim_size"/>
+            <output name="chimera" file="empty_file_3.bam" ftype="bam" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[