Mercurial > repos > iuc > idba_ud

annotate idba_ud.xml @ 1:2ed5c0795f99 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
author iuc
date Mon, 05 Aug 2019 15:59:42 -0400
parents fdaf2375d405
children 694b0f55b744
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2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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1 <tool id="idba_ud" name="IDBA-UD" version="@IDBA_VERSION@+galaxy1">
0
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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2 <description>
1
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3 Iterative de Bruijn Graph Assembler for data with highly uneven depth
0
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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7 </macros>
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8 <expand macro="requirements"/>
1
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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9 <command detect_errors="aggressive"><![CDATA[
0
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10 idba_ud
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11
1
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12 @MAIN_INPUT@
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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13 @LEVELS_INPUT@
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14 @KMER_OPTIONS@
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15 @FILTER_OPTIONS@
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16 --min_pairs $min_pairs
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17 @OTHER_OPTIONS@
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18 @THREADS@
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19 ]]></command>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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20
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21 <inputs>
1
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22 <expand macro="main_input"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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23 <expand macro="levels_input"/>
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24 <expand macro="kmer_options" maxk_default="100" step_default="20"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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25 <expand macro="filter_options"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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26 <expand macro="min_pairs_filter"/>
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27 <expand macro="other_options">
0
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28 <option value="--no_bubble">Do not merge bubble (--no_bubble)</option>
1
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29 </expand>
0
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30 </inputs>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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31 <outputs>
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32 <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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33 </outputs>
fdaf2375d405 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 6901a5d3feb96ea81d2e3b765b39e32cb94565eb
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34 <tests>
1
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35 <!-- basic test + check of defaults -->
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36 <test>
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37 <param name="read" value="merged.fa" ftype="fasta"/>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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38 <assert_command>
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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39 <has_text text="--mink 20" />
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40 <has_text text="--maxk 100" />
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41 <has_text text="--step 20" />
2ed5c0795f99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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42 <has_text text="--inner_mink 10" />
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43 <has_text text="--inner_step 5" />
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44 <has_text text="--prefix 3" />
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45 <has_text text="--min_count 2" />
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46 <has_text text="--min_support 1" />
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47 <has_text text="--seed_kmer 30" />
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48 <has_text text="--min_contig 200" />
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49 <has_text text="--similar 0.95" />
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50 <has_text text="--max_mismatch 3" />
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51 <has_text text="--min_pairs 3" />
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52 <not_has_text text="--read_level_2" />
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53 <not_has_text text="--read_level_3" />
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54 <not_has_text text="--read_level_4" />
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55 <not_has_text text="--read_level_5" />
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56 <not_has_text text="--no_bubble" />
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57 <not_has_text text="--no_local" />
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58 <not_has_text text="--no_coverage" />
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59 <not_has_text text="--no_correct" />
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60 <not_has_text text="--pre_correction" />
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61 </assert_command>
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62 <output name="output" file="out/scaffold.fa" ftype="fasta"/>
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63 </test>
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64 <!-- read levels test -->
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65 <test>
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66 <param name="read" value="merged.fa" ftype="fasta"/>
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67 <param name="read_level_2" ftype="fasta" value="merged.fa"/>
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68 <param name="read_level_3" ftype="fasta" value="merged.fa"/>
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69 <param name="read_level_4" ftype="fasta" value="merged.fa"/>
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70 <param name="read_level_5" ftype="fasta" value="merged.fa"/>
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71 <assert_command>
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72 <has_text text="--read_level_2" />
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73 <has_text text="--read_level_3" />
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74 <has_text text="--read_level_4" />
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75 <has_text text="--read_level_5" />
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76 </assert_command>
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77 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="sim_size"/>
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78 </test>
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79 <!-- k-mer options -->
0
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80 <test>
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81 <param name="read" value="merged.fa" ftype="fasta"/>
1
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82 <param name="mink" value="19"/>
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83 <param name="maxk" value="99"/>
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84 <param name="step" value="19"/>
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85 <param name="inner_mink" value="9"/>
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86 <param name="inner_step" value="4"/>
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87 <param name="prefix" value="2"/>
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88 <param name="min_count" value="1"/>
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89 <param name="min_support" value="2"/>
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90 <param name="seed_kmer" value="29"/>
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91 <assert_command>
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92 <has_text text="--mink 19" />
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93 <has_text text="--maxk 99" />
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94 <has_text text="--step 19" />
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95 <has_text text="--inner_mink 9" />
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96 <has_text text="--inner_step 4" />
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97 <has_text text="--prefix 2" />
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98 <has_text text="--min_count 1" />
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99 <has_text text="--min_support 2" />
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100 <has_text text="--seed_kmer 29" />
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101 </assert_command>
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102 <output name="output" file="out/scaffold.fa" compare="sim_size"/>
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103 </test>
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104 <!-- filter options -->
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105 <test>
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106 <param name="read" value="merged.fa" ftype="fasta"/>
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107 <param name="min_contig" value="199"/>
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108 <param name="similar" value="0.96"/>
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109 <param name="max_mismatch" value="2"/>
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110 <assert_command>
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111 <has_text text="--min_contig 199" />
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112 <has_text text="--similar 0.96" />
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113 <has_text text="--max_mismatch 2" />
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114 </assert_command>
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115 <output name="output" file="out/scaffold.fa" compare="sim_size"/>
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116 </test>
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117 <!-- min-pairs and other options -->
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118 <test>
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119 <param name="read" value="merged.fa" ftype="fasta"/>
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120 <param name="min_pairs" value="2"/>
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121 <param name="other" value="--no_bubble,--no_local,--no_coverage,--no_correct,--pre_correction"/>
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122 <assert_command>
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123 <has_text text="--min_pairs 2" />
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124 <has_text text="--no_bubble" />
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125 <has_text text="--no_local" />
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126 <has_text text="--no_coverage" />
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127 <has_text text="--no_correct" />
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128 <has_text text="--pre_correction" />
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129 </assert_command>
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130 <output name="output" file="out/scaffold.fa" compare="sim_size"/>
0
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131 </test>
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132 </tests>
1
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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."/>
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134 <expand macro="citations">
0
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135 <citation type="doi">10.1093/bioinformatics/bts174</citation>
1
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136 </expand>
0
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137 </tool>