diff busco.xml @ 20:ea8146ee148f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 9bf18dbcef34a48d3c40150ee953706bececfdd1

--- a/busco.xml	Tue Nov 14 13:03:37 2023 +0000
+++ b/busco.xml	Mon Mar 18 16:01:49 2024 +0000
@@ -209,7 +209,7 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,gff" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_gff">
                 <assert_contents>
@@ -233,7 +233,7 @@
                 <param name="mode" value="prot" />
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum" file="proteome_results/short_summary" compare="re_match_multiline" />
             <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
             <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
@@ -254,7 +254,7 @@
                 <param name="mode" value="tran" />
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum" file="transcriptome_results/short_summary" compare="re_match_multiline" />
             <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
             <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
@@ -278,7 +278,7 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,gff" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/>
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_gff">
                 <assert_contents>
@@ -306,7 +306,7 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
         </test>
@@ -323,11 +323,15 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="re_match_multiline" />
             <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
             <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
-            <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
+            <output name="busco_gff" ftype="gff3">
+                <assert_contents>
+                    <has_n_lines n="13"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
@@ -343,7 +347,7 @@
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
             <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
+            <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
             <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
             <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />