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changeset 4:9feed355ea6d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
author iuc
date Thu, 21 Jul 2022 13:32:22 +0000
parents d7dd10b4f269
children
files idba_ud.xml test-data/out/scaffold.fa
diffstat 2 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/idba_ud.xml	Tue Aug 31 09:04:36 2021 +0000
+++ b/idba_ud.xml	Thu Jul 21 13:32:22 2022 +0000
@@ -60,7 +60,7 @@
                 <not_has_text text="--no_correct" />
                 <not_has_text text="--pre_correction" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" ftype="fasta"/>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
         </test>
         <!-- read levels test -->
         <test>
@@ -75,7 +75,7 @@
                 <has_text text="--read_level_4" />
                 <has_text text="--read_level_5" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" ftype="fasta" lines_diff="2"/>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
         </test>
         <!-- k-mer options -->
         <test>
@@ -100,7 +100,7 @@
                 <has_text text="--min_support 2" />
                 <has_text text="--seed_kmer 29" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
+            <output name="output" file="out/scaffold.fa" compare="re_match"/>
         </test>
         <!-- filter options -->
         <test>
@@ -113,7 +113,7 @@
                 <has_text text="--similar 0.96" />
                 <has_text text="--max_mismatch 2" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
+            <output name="output" file="out/scaffold.fa" compare="re_match"/>
         </test>
         <!-- min-pairs and other options -->
         <test>
@@ -128,7 +128,7 @@
                 <has_text text="--no_correct" />
                 <has_text text="--pre_correction" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
+            <output name="output" file="out/scaffold.fa" compare="re_match"/>
         </test>
     </tests>
     <expand macro="help" more_help="IDBA-UD is an extension of IDBA algorithm for Short Reads Sequencing data with Highly Uneven Sequencing Depth. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions."/>
--- a/test-data/out/scaffold.fa	Tue Aug 31 09:04:36 2021 +0000
+++ b/test-data/out/scaffold.fa	Thu Jul 21 13:32:22 2022 +0000
@@ -1,2 +1,2 @@
 >scaffold_0
-GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA
+[ATCG]+
\ No newline at end of file