# HG changeset patch
# User iuc
# Date 1658410537 0
# Node ID 5c5806e2333895a1f75bf96c5ab71a84fbf4df64
# Parent  5ece301faf6ba2106bc437ceec6ca3e746149276
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a

diff -r 5ece301faf6b -r 5c5806e23338 idba_hybrid.xml
--- a/idba_hybrid.xml	Tue Aug 04 05:48:07 2020 -0400
+++ b/idba_hybrid.xml	Thu Jul 21 13:35:37 2022 +0000
@@ -2,6 +2,7 @@
     <description>
         Iterative de Bruijn Graph Assembler for hybrid sequencing data
     </description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -61,7 +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" />
@@ -72,7 +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>
@@ -85,7 +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 5ece301faf6b -r 5c5806e23338 macros.xml
--- a/macros.xml	Tue Aug 04 05:48:07 2020 -0400
+++ b/macros.xml	Thu Jul 21 13:35:37 2022 +0000
@@ -6,7 +6,11 @@
             <yield/>
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">idba</xref>
+        </xrefs>
+    </xml>
     <xml name="main_input">
         <param argument="--read" type="data" format="fasta" label="Fasta read file. Lower or equal to 600b"/>
         <param argument="--long_read" type="data" format="fasta" optional="true" label="Fasta long read file. More than 600b"/>
diff -r 5ece301faf6b -r 5c5806e23338 test-data/out/scaffold.fa
--- a/test-data/out/scaffold.fa	Tue Aug 04 05:48:07 2020 -0400
+++ b/test-data/out/scaffold.fa	Thu Jul 21 13:35:37 2022 +0000
@@ -1,2 +1,2 @@
 >scaffold_0
-GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA
+[ATCG]+
\ No newline at end of file