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changeset 2:694b0f55b744 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
author iuc
date Tue, 04 Aug 2020 05:50:30 -0400
parents 2ed5c0795f99
children 1542a2fffe0c
files idba_ud.xml test-data/out/contig.fa
diffstat 2 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/idba_ud.xml	Mon Aug 05 15:59:42 2019 -0400
+++ b/idba_ud.xml	Tue Aug 04 05:50:30 2020 -0400
@@ -74,7 +74,7 @@
                 <has_text text="--read_level_4" />
                 <has_text text="--read_level_5" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/>
+            <output name="output" file="out/scaffold.fa" ftype="fasta" lines_diff="2"/>
         </test>
         <!-- k-mer options -->
         <test>
@@ -99,7 +99,7 @@
                 <has_text text="--min_support 2" />
                 <has_text text="--seed_kmer 29" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" compare="sim_size"/>
+            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
         </test>
         <!-- filter options -->
         <test>
@@ -112,7 +112,7 @@
                 <has_text text="--similar 0.96" />
                 <has_text text="--max_mismatch 2" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" compare="sim_size"/>
+            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
         </test>
         <!-- min-pairs and other options -->
         <test>
@@ -127,7 +127,7 @@
                 <has_text text="--no_correct" />
                 <has_text text="--pre_correction" />
             </assert_command>
-            <output name="output" file="out/scaffold.fa" compare="sim_size"/>
+            <output name="output" file="out/scaffold.fa" lines_diff="2"/>
         </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/contig.fa	Mon Aug 05 15:59:42 2019 -0400
+++ b/test-data/out/contig.fa	Tue Aug 04 05:50:30 2020 -0400
@@ -1,2 +1,2 @@
->contig-100_0 length_749 read_count_0
-GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA
+>contig-60_0 length_749 read_count_302
+TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC