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comparison idba_ud.xml @ 3:1542a2fffe0c 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 13:34:59 +0000
parents 694b0f55b744
children
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2:694b0f55b744 3:1542a2fffe0c
1 <tool id="idba_ud" name="IDBA-UD" version="@IDBA_VERSION@+galaxy1"> 1 <tool id="idba_ud" name="IDBA-UD" version="@IDBA_VERSION@+galaxy1">
2 <description> 2 <description>
3 Iterative de Bruijn Graph Assembler for data with highly uneven depth 3 Iterative de Bruijn Graph Assembler for data with highly uneven depth
4 </description> 4 </description>
5 <expand macro="bio_tools"/>
5 <macros> 6 <macros>
6 <import>macros.xml</import> 7 <import>macros.xml</import>
7 </macros> 8 </macros>
8 <expand macro="requirements"/> 9 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
57 <not_has_text text="--no_local" /> 58 <not_has_text text="--no_local" />
58 <not_has_text text="--no_coverage" /> 59 <not_has_text text="--no_coverage" />
59 <not_has_text text="--no_correct" /> 60 <not_has_text text="--no_correct" />
60 <not_has_text text="--pre_correction" /> 61 <not_has_text text="--pre_correction" />
61 </assert_command> 62 </assert_command>
62 <output name="output" file="out/scaffold.fa" ftype="fasta"/> 63 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
63 </test> 64 </test>
64 <!-- read levels test --> 65 <!-- read levels test -->
65 <test> 66 <test>
66 <param name="read" value="merged.fa" ftype="fasta"/> 67 <param name="read" value="merged.fa" ftype="fasta"/>
67 <param name="read_level_2" ftype="fasta" value="merged.fa"/> 68 <param name="read_level_2" ftype="fasta" value="merged.fa"/>
72 <has_text text="--read_level_2" /> 73 <has_text text="--read_level_2" />
73 <has_text text="--read_level_3" /> 74 <has_text text="--read_level_3" />
74 <has_text text="--read_level_4" /> 75 <has_text text="--read_level_4" />
75 <has_text text="--read_level_5" /> 76 <has_text text="--read_level_5" />
76 </assert_command> 77 </assert_command>
77 <output name="output" file="out/scaffold.fa" ftype="fasta" lines_diff="2"/> 78 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/>
78 </test> 79 </test>
79 <!-- k-mer options --> 80 <!-- k-mer options -->
80 <test> 81 <test>
81 <param name="read" value="merged.fa" ftype="fasta"/> 82 <param name="read" value="merged.fa" ftype="fasta"/>
82 <param name="mink" value="19"/> 83 <param name="mink" value="19"/>
97 <has_text text="--prefix 2" /> 98 <has_text text="--prefix 2" />
98 <has_text text="--min_count 1" /> 99 <has_text text="--min_count 1" />
99 <has_text text="--min_support 2" /> 100 <has_text text="--min_support 2" />
100 <has_text text="--seed_kmer 29" /> 101 <has_text text="--seed_kmer 29" />
101 </assert_command> 102 </assert_command>
102 <output name="output" file="out/scaffold.fa" lines_diff="2"/> 103 <output name="output" file="out/scaffold.fa" compare="re_match"/>
103 </test> 104 </test>
104 <!-- filter options --> 105 <!-- filter options -->
105 <test> 106 <test>
106 <param name="read" value="merged.fa" ftype="fasta"/> 107 <param name="read" value="merged.fa" ftype="fasta"/>
107 <param name="min_contig" value="199"/> 108 <param name="min_contig" value="199"/>
110 <assert_command> 111 <assert_command>
111 <has_text text="--min_contig 199" /> 112 <has_text text="--min_contig 199" />
112 <has_text text="--similar 0.96" /> 113 <has_text text="--similar 0.96" />
113 <has_text text="--max_mismatch 2" /> 114 <has_text text="--max_mismatch 2" />
114 </assert_command> 115 </assert_command>
115 <output name="output" file="out/scaffold.fa" lines_diff="2"/> 116 <output name="output" file="out/scaffold.fa" compare="re_match"/>
116 </test> 117 </test>
117 <!-- min-pairs and other options --> 118 <!-- min-pairs and other options -->
118 <test> 119 <test>
119 <param name="read" value="merged.fa" ftype="fasta"/> 120 <param name="read" value="merged.fa" ftype="fasta"/>
120 <param name="min_pairs" value="2"/> 121 <param name="min_pairs" value="2"/>
125 <has_text text="--no_local" /> 126 <has_text text="--no_local" />
126 <has_text text="--no_coverage" /> 127 <has_text text="--no_coverage" />
127 <has_text text="--no_correct" /> 128 <has_text text="--no_correct" />
128 <has_text text="--pre_correction" /> 129 <has_text text="--pre_correction" />
129 </assert_command> 130 </assert_command>
130 <output name="output" file="out/scaffold.fa" lines_diff="2"/> 131 <output name="output" file="out/scaffold.fa" compare="re_match"/>
131 </test> 132 </test>
132 </tests> 133 </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."/> 134 <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"> 135 <expand macro="citations">
135 <citation type="doi">10.1093/bioinformatics/bts174</citation> 136 <citation type="doi">10.1093/bioinformatics/bts174</citation>