| Previous changeset 1:2ed5c0795f99 (2019-08-05) Next changeset 3:1542a2fffe0c (2022-07-21) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37" |
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modified:
idba_ud.xml test-data/out/contig.fa |
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| diff -r 2ed5c0795f99 -r 694b0f55b744 idba_ud.xml --- a/idba_ud.xml Mon Aug 05 15:59:42 2019 -0400 +++ b/idba_ud.xml Tue Aug 04 05:50:30 2020 -0400 |
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| @@ -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."/> |
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| diff -r 2ed5c0795f99 -r 694b0f55b744 test-data/out/contig.fa --- 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 |
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| @@ -1,2 +1,2 @@ ->contig-100_0 length_749 read_count_0 -GAAAAACGCGCTTGCAGATGGGTCGCAGGTTACTTCCTTGCGCACAGGATATAGTTATACCAGCGTTATTGTCGTTAGTGGTGAGTCGTCGGTATATCTGAATGGAGATACGACAATCAGCGGAGAATTCCCTCTGGGGTTTGCCGGGGTTATTCGGGTACAGGATAAAGCTTTGCTGGAAATTGGCAGTGGCGCTACGCTAACAATGCAGGATATTGACAGTTTTGAACATCATGGGACAAGAACCCTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCTGCCGTTAACCCGTCTGGTTTGGGCATGATACTGATGTAGTCACGCTTTATCGTTTTCACGAAGCTCTCTGCTATTCCGTTACTCTCCGGACTCCGCACCGCCGTGTTCTTCGGTTCAAGTCCCAACATCCGGGCGAACTGGCGTGTTTCATTAGCCCGGTAGCATGAACCATTATCCGTCAGCCACTCCACTGGAGACGACGGAAGATCGTTGCCGAAGCGGCGTTCCACCGCTCCCAGCATGACGTCCTGTACTGTTTCACTGTTGAAGCCGCCGGTAGTGACCGCCCAGTGCAGTGCCTCACGATCACAGCAGTCCAGCGCGAACGTGACACGCAGTCTCTCTCCGTTA +>contig-60_0 length_749 read_count_302 +TAACGGAGAGAGACTGCGTGTCACGTTCGCGCTGGACTGCTGTGATCGTGAGGCACTGCACTGGGCGGTCACTACCGGCGGCTTCAACAGTGAAACAGTACAGGACGTCATGCTGGGAGCGGTGGAACGCCGCTTCGGCAACGATCTTCCGTCGTCTCCAGTGGAGTGGCTGACGGATAATGGTTCATGCTACCGGGCTAATGAAACACGCCAGTTCGCCCGGATGTTGGGACTTGAACCGAAGAACACGGCGGTGCGGAGTCCGGAGAGTAACGGAATAGCAGAGAGCTTCGTGAAAACGATAAAGCGTGACTACATCAGTATCATGCCCAAACCAGACGGGTTAACGGCAGCAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCAGGGTTCTTGTCCCATGATGTTCAAAACTGTCAATATCCTGCATTGTTAGCGTAGCGCCACTGCCAATTTCCAGCAAAGCTTTATCCTGTACCCGAATAACCCCGGCAAACCCCAGAGGGAATTCTCCGCTGATTGTCGTATCTCCATTCAGATATACCGACGACTCACCACTAACGACAATAACGCTGGTATAACTATATCCTGTGCGCAAGGAAGTAACCTGCGACCCATCTGCAAGCGCGTTTTTC |