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annotate wtdbg.xml @ 0:6a060928f7ff draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
author bgruening
date Tue, 12 Jun 2018 13:40:49 -0400
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children e100f3f4d80e
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0
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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1 <tool id="wtdbg" name="WTDBG" version="1.2.8.1">
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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2 <description>De novo assembler AND consensuser for long noisy sequences</description>
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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3 <macros>
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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4 <import>macros.xml</import>
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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5 </macros>
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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6 <expand macro="requirements" />
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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7 <version_command>wtdbg -help | grep 'Version:'</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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9 wtdbg
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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10 -t \${GALAXY_SLOTS:-4}
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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11 -i $i
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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12 -o 'dbg'
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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13 #if $I:
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14 -I '$I'
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15 #end if
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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16 #if $load_alignments:
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17 --load-alignments '$load_alignments'
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18 #end if
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19
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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20 -k $k
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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21 -p $p
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22 -K $K
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23 -E $E
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24 $F
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25 -S $S
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26 -X $X
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27 -Y $Y
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28 -x $x
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29 -y $y
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30 -l $l
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31 -m $m
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32 -s $s
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33 --tidy-reads $tidy_reads
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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34 --edge-min $edge_min
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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35 $rescue_low_cov_edges
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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36 &&
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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37 wtdbg-cns
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38 -t \${GALAXY_SLOTS:-4}
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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39 -o dbg.ctg.lay.fa
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40 -i dbg.ctg.lay
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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41 -j $cns.j
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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42 -k $cns.k
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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43 -Z $cns.Z
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44 -W $cns.W
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45 -H $cns.H
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46 -L $cns.L
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47 -c $cns.c
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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48 -M $cns.M
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49 -X $cns.X
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50 -I $cns.I
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51 -D $cns.D
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52 -E $cns.E
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53 -m $cns.m
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54 -S $cns.S
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55
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56 ]]></command>
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57 <inputs>
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58 <param type="data" argument="-i" format="fasta,fasta.gz" label="Long reads sequences file"/>
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59 <param type="data" argument="-I" format="fasta,fasta.gz" optional="True" label="Error-free sequences file"/>
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60 <param type="data" argument="--load-alignments" name="load_alignments" format="tabular" optional="True" label="Load pre-computed alignments"/>
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61
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62 <param argument="k" type="integer" value="0" min="0" max="25" label="Kmer fsize" />
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63 <param argument="p" type="integer" value="21" min="0" max="25" label="Kmer psize" />
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64 <param argument="K" type="float" value="1000" min="0" max="65535" label="Filter high frequency kmers" />
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65 <param argument="E" type="integer" value="2" label="Min kmer frequency" />
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66 <param argument="F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Filter low frequency kmers by a 4G-bytes array" />
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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67 <param argument="S" type="integer" value="4" label="Subsampling kmers, 1/S kmers are indexed" />
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68 <param argument="X" type="integer" value="4" label="Max number of bin (256bp) in one gap" />
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69 <param argument="Y" type="integer" value="4" label="Max number of bin (256bp) in one deviation" />
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70 <param argument="x" type="integer" value="-7" label="penalty for BIN gap" />
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71 <param argument="y" type="integer" value="-21" label="penalty for BIN deviation" />
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72 <param argument="l" type="float" value="2048" min="1" label="Min length of alignment" />
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73 <param argument="m" type="float" value="200" label="Min matched" />
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74 <param argument="s" type="float" value="0.2" label="Max length variation of two aligned fragments" />
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75
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76 <param argument="--tidy-reads" name="tidy_reads" type="integer" value="0" label="Filter reads less than tidy-reads" />
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77 <param argument="--edge-min" name="edge_min" type="integer" value="3" label="The minimal depth of a valid edge set to" />
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78 <param argument="--rescue-low-cov-edges" name="rescue_low_cov_edges" type="boolean" truevalue="--rescue-low-cov-edges"
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79 falsevalue="" label="Try to rescue low coverage edges" />
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80
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81 <section name="cns" title="Consensus options">
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82 <!-- optional inputs -->
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83 <!-- <param argument="-i" type="data" format="utg.cns" label="Input file(s) *.utg.cns" /> -->
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84
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85 <param argument="-j" type="integer" value="1000" label="Expected length of node" />
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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86 <param argument="-k" type="integer" value="15" label="Kmer size for long reads" />
6a060928f7ff planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit c97be39112be9dc6118a3e12e51dcb15ed554274
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87 <param argument="-Z" type="integer" value="4" label="Z-cutoff, drop the lower" />
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88 <param argument="-W" type="integer" value="48" label="W-cutoff, drop the lagger (position)" />
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89 <param argument="-H" type="integer" value="1" label="High coverage bonus" />
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90 <param argument="-L" type="integer" value="10" label="High coverage cutoff" />
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91 <param argument="-c" type="select" label="Candidate strategy">
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92 <option value="0" selected="true">best-kmers</option>
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93 <option value="1" >median length</option>
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94 <option value="2" >first (include)</option>
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95 <option value="3" >first (exclude)</option>
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96 <option value="4" >longest</option>
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97 <option value="5" >shortest</option>
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98 </param>
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99
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100 <param argument="-M" type="integer" value="2" label="Match score" />
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101 <param argument="-X" type="integer" value="-7" label="Mismatch score" />
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102 <param argument="-I" type="integer" value="-3" label="Insertion score" />
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103 <param argument="-D" type="integer" value="-4" label="Deletion score" />
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104 <param argument="-E" type="integer" value="-2" label="Gap extension score" />
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105 <param argument="-m" type="select" label="Correction mode">
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106 <option value="1" selected="true">DBG correction</option>
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107 <option value="2" >DAG correction</option>
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108 </param>
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109 <param argument="-S" type="integer" value="1" label="Correct structure before error correction" />
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110 </section>
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111
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112 </inputs>
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113 <outputs>
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114 <data name="output_alignments" format="fasta" label="${tool.name} alignments" from_work_dir="dbg.alignments" />
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115 <data name="output_ctglay" format="txt" label="${tool.name} contigs layout" from_work_dir="dbg.ctg.lay" />
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116 <data name="output_consensus" format="fasta" label="${tool.name} consensus" from_work_dir="dbg.ctg.lay.fa" />
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117 </outputs>
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118 <tests>
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119 <test>
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120 <param name="i" value="ecoli-reads.fa"/>
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121 <output name="output_alignments" file="result1.alignments"/>
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122 <output name="output_ctglay" file="result1.ctg.lay"/>
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123 <output name="output_consensus" file="consensus_result1.fa"/>
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124 </test>
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125 <test>
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126 <param name="i" value="ecoli-reads.fa"/>
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127 <param name="tidy_reads" value="5000"/>
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128 <param name="edge_min" value="2"/>
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129 <param name="rescue_low_cov_edges" value="True"/>
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130 <output name="output_consensus" file="consensus_result2.fa"/>
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131 </test>
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132 <test>
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133 <param name="i" value="ecoli-reads.fa"/>
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134 <param name="cns.c" value="1"/>
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135 <param name="cns.E" value="-3"/>
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136 <param name="cns.j" value="500"/>
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137 <param name="cns.m" value="2"/>
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138 <param name="cns.k" value="5"/>
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139 <output name="output_consensus" file="consensus_result3.fa"/>
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140 </test>
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141
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142 </tests>
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143
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144 <help><![CDATA[
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145 **What it does**
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146
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147 WTDBG is a de novo assembler for long noisy sequences, based on fuzzy Bruijn graphs (FBG).
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148
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149 **Alignment**
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150
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151 KBM (Kmer-BIN-Mapping) groups k-mers from each non-overlapped sliding 256 bp fragments in long reads into bins.
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152 Bins of which most k-mers are high frequency, are filtered as highly repetitive ones.
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153 Then, KBM searches synteny of matched bin pairs in sequences in a dynamic programming way.
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154 A matched bin pair in two sequences is defined as two bins different by original but share a set of k-mers.
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155 The result of alignments in KBM have the same features of traditional sequence alignment, excepting the unit of
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156 KBM alignments is 256 bp bin instead of single base.
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157
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158 **Assembly**
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159
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160 FBG (Fuzzy Bruijn Graph) is composed of vertices in length of 1024 bp from reads, and edges connecting vertices
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161 in their order on read paths. Comparing with DBG, the size of vertices in FBG are much bigger, thus won't be
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162 sensitive to small repeat. To tolerate high sequencing errors, FBG's vertices are found using gapped
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163 sequence alignments from KBM or other aligners, comparing with searching identical k-mers in DBG.
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164
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165 ]]></help>
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166 <expand macro="citations" />
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167 </tool>