# HG changeset patch
# User iuc
# Date 1658410388 0
# Node ID d6ad088a48e7421e98c3be9ece2383e29c38808e
# Parent  368a9a2fea808a49dd0e0148843032ed0d41ad34
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a

diff -r 368a9a2fea80 -r d6ad088a48e7 idba_hybrid.xml
--- a/idba_hybrid.xml	Tue Aug 31 09:05:38 2021 +0000
+++ b/idba_hybrid.xml	Thu Jul 21 13:33:08 2022 +0000
@@ -62,7 +62,7 @@
             <param name="ref_source|reference" value="reference.fa" ftype="fasta"/>
             <param name="ref_source|ref_source_sel" value="history"/>
             <param name="read" value="merged.fa" ftype="fasta"/>
-            <output name="output" file="out/scaffold.fa" ftype="fasta"/>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
             <assert_command>
                 <has_text text="--min_region 300" />
                 <has_text text="--max_gap 3" />
@@ -73,7 +73,7 @@
             <param name="ref_source|reference" value="test_id"/>
             <param name="ref_source|ref_source_sel" value="cached"/>
             <param name="read" value="merged.fa" ftype="fasta"/>
-            <output name="output" file="out/scaffold.fa" ftype="fasta"/>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
         </test>
         <!-- tool specific parameters -->
         <test>
@@ -86,7 +86,7 @@
                 <has_text text="--min_region 299" />
                 <has_text text="--max_gap 2" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" ftype="fasta"/>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
         </test>
     </tests>
     <expand macro="help" more_help="IDBA-Hybrid is an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing. It is an extension of IDBA-UD algorithm. It aims at using a closed related reference genome to help de novo assembly, especially when sequencing depth is low. IDBA-Hybrid does alignment between reads and reference first to extract similar regions in the reference genome, and then it correct the similar regions based on the alignment results and apply local assembly technique to resolve potential structure virations. Finally, it groups all the reads and the contigs got from those similar regions to do de novo assembly. The expriments showed it outperforms all existing de novo or hybrid assembly algorithms, especilly when the sequencing depth is low and the reference genome is similar to the target genome."/>
diff -r 368a9a2fea80 -r d6ad088a48e7 test-data/out/scaffold.fa
--- a/test-data/out/scaffold.fa	Tue Aug 31 09:05:38 2021 +0000
+++ b/test-data/out/scaffold.fa	Thu Jul 21 13:33:08 2022 +0000
@@ -1,2 +1,2 @@
 >scaffold_0
-GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA
+[ATCG]+
\ No newline at end of file