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comparison idba_ud.xml @ 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
comparison
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1:2ed5c0795f99 2:694b0f55b744
72 <has_text text="--read_level_2" /> 72 <has_text text="--read_level_2" />
73 <has_text text="--read_level_3" /> 73 <has_text text="--read_level_3" />
74 <has_text text="--read_level_4" /> 74 <has_text text="--read_level_4" />
75 <has_text text="--read_level_5" /> 75 <has_text text="--read_level_5" />
76 </assert_command> 76 </assert_command>
77 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/> 77 <output name="output" file="out/scaffold.fa" ftype="fasta" lines_diff="2"/>
78 </test> 78 </test>
79 <!-- k-mer options --> 79 <!-- k-mer options -->
80 <test> 80 <test>
81 <param name="read" value="merged.fa" ftype="fasta"/> 81 <param name="read" value="merged.fa" ftype="fasta"/>
82 <param name="mink" value="19"/> 82 <param name="mink" value="19"/>
97 <has_text text="--prefix 2" /> 97 <has_text text="--prefix 2" />
98 <has_text text="--min_count 1" /> 98 <has_text text="--min_count 1" />
99 <has_text text="--min_support 2" /> 99 <has_text text="--min_support 2" />
100 <has_text text="--seed_kmer 29" /> 100 <has_text text="--seed_kmer 29" />
101 </assert_command> 101 </assert_command>
102 <output name="output" file="out/scaffold.fa" compare="sim_size"/> 102 <output name="output" file="out/scaffold.fa" lines_diff="2"/>
103 </test> 103 </test>
104 <!-- filter options --> 104 <!-- filter options -->
105 <test> 105 <test>
106 <param name="read" value="merged.fa" ftype="fasta"/> 106 <param name="read" value="merged.fa" ftype="fasta"/>
107 <param name="min_contig" value="199"/> 107 <param name="min_contig" value="199"/>
110 <assert_command> 110 <assert_command>
111 <has_text text="--min_contig 199" /> 111 <has_text text="--min_contig 199" />
112 <has_text text="--similar 0.96" /> 112 <has_text text="--similar 0.96" />
113 <has_text text="--max_mismatch 2" /> 113 <has_text text="--max_mismatch 2" />
114 </assert_command> 114 </assert_command>
115 <output name="output" file="out/scaffold.fa" compare="sim_size"/> 115 <output name="output" file="out/scaffold.fa" lines_diff="2"/>
116 </test> 116 </test>
117 <!-- min-pairs and other options --> 117 <!-- min-pairs and other options -->
118 <test> 118 <test>
119 <param name="read" value="merged.fa" ftype="fasta"/> 119 <param name="read" value="merged.fa" ftype="fasta"/>
120 <param name="min_pairs" value="2"/> 120 <param name="min_pairs" value="2"/>
125 <has_text text="--no_local" /> 125 <has_text text="--no_local" />
126 <has_text text="--no_coverage" /> 126 <has_text text="--no_coverage" />
127 <has_text text="--no_correct" /> 127 <has_text text="--no_correct" />
128 <has_text text="--pre_correction" /> 128 <has_text text="--pre_correction" />
129 </assert_command> 129 </assert_command>
130 <output name="output" file="out/scaffold.fa" compare="sim_size"/> 130 <output name="output" file="out/scaffold.fa" lines_diff="2"/>
131 </test> 131 </test>
132 </tests> 132 </tests>
133 <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."/> 133 <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."/>
134 <expand macro="citations"> 134 <expand macro="citations">
135 <citation type="doi">10.1093/bioinformatics/bts174</citation> 135 <citation type="doi">10.1093/bioinformatics/bts174</citation>