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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yaha commit 442d981e7d3a5634063cfc26bc29c83d88d697cd-dirty
author mvdbeek
date Thu, 05 Jan 2017 08:24:22 -0500
parents bcba667aef5b
children
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1 <tool id="yaha" name="yaha" version="0.1.83">
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2 <description>fast and flexible long-read alignment with optimal breakpoint detection</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.1.83">yaha</requirement>
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8 <requirement type="package" version="0.6.5">sambamba</requirement>
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9 </requirements>
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10 <version_command><![CDATA[yaha 2>&1| head -n1]]></version_command>
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11 <command detect_errors="aggressive"><![CDATA[
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12 #if $reference_genome.reference_genome_source == "history" or "reference":
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13 #if $reference_genome.reference_genome_source == "history":
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14 ln -f -s "$reference_genome.history_item" genome.fa &&
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15 #elif $reference_genome.reference_genome_source == "reference":
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16 ln -f -s "$reference_genome.fasta_item.fields.path" genome.fa &&
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17 #end if
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18 yaha -g genome.fa -H $reference_genome.maxHitsIndex -L $reference_genome.wordLenIndex -S $reference_genome.skipDistanceIndex &&
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19 #set maxHitsIndex = "%s%s" % ("0" * (5 - len(str($reference_genome.maxHitsIndex))), $reference_genome.maxHitsIndex)
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20 #set skipdist = $reference_genome.skipDistanceIndex if len(str($reference_genome.skipDistanceIndex)) > 1 else "0%s" % $reference_genome.skipDistanceIndex
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21 #set wordLenIndex = $reference_genome.wordLenIndex if len(str($reference_genome.wordLenIndex)) > 1 else "0%s" % $reference_genome.wordLenIndex
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22 #set index_path = "genome.X%s_%s_%sS" % ($wordLenIndex, $skipdist, $maxHitsIndex)
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23 #else:
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24 #pass ## augment with pre-built index if considered useful
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25 #end if
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26 yaha
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27 -x '$index_path'
3
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28 #if str($readtype.single_or_paired) == "se":
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29 -q '$readtype.input_single'
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30 #else:
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31 -q <(cat '$readtype.input_paired.forward' '$readtype.input_paired.reverse')
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32 #end if
0
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33 $outformat stdout
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34 -t \${GALAXY_SLOTS:-1}
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35 -BW $BW
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36 -G $G
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37 -H $H
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38 -M $M
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39 -MD $MD
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40 -P $P
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41 -X $X
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42 #if $ags.use_ags == "yes":
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43 -AGS Y
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44 -GEC $ags.GEC
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45 -GOC $ags.GOC
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46 -MS $ags.MS
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47 -RC $ags.RC
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48 #else:
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49 -AGS N
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50 #end if
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51 #if $oqc.use_oqc == "yes":
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52 -OQC Y
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53 -BP $oqc.BP
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54 -MGDP $oqc.MGDP
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55 -MNO $oqc.MNO
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56 #else:
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57 -OQC N
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58 #end if
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59 #if $fbs.use_fbs == "yes":
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60 -FBS Y
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61 -PRL $fbs.PRL
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62 -PSS $fbs.PSS
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63 #else:
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64 -FBS N
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65 #end if
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66 | sambamba view -S -f bam /dev/stdin | sambamba sort -o '$alignment' -l 6 -t \${GALAXY_SLOTS:-1} /dev/stdin
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67 ]]></command>
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68 <inputs>
3
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69 <conditional name="readtype">
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70 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: yaha does not take mate-pair information into account. If you select pe_collection, forward and reverse reads will be merged.">
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71 <option value="se" selected="true">Single-end</option>
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72 <option value="pe_collection">Paired-end (as collection)</option>
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73 </param>
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74 <when value="se">
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75 <param format="fastqsanger,fastqsanger.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-q)" />
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76 </when>
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77 <when value="pe_collection">
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78 <param format="fastqsanger,fastqsanger.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" help="(-q)"/>
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79 </when>
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80 </conditional>
0
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81 <conditional name="reference_genome">
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82 <param help="Built-in references were created using default options" label="Source for the reference genome to align against" name="reference_genome_source" type="select">
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83 <!-- Write a datamanager if prebuilt genomes are important
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84 <option selected="True" value="indexed">Use a built-in index</option>
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85 -->
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86 <option value="history">Use a genome from history to build an index</option>
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87 <option value="reference">Use a built-in genome to build an index</option>
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88 </param>
3
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89 <!--
0
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90 <when value="indexed">
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91 <param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="index" type="select">
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92 <options from_data_table="yaha_indexes">
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93 <filter column="2" type="sort_by" />
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94 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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95 </options>
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96 </param>
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97 </when>
3
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98 -->
0
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99 <when value="history">
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100 <param format="fasta" label="Select the reference genome" name="history_item" type="data" />
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101 <expand macro="index_parameter"/>
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102 </when>
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103 <when value="reference">
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104 <param label="Select a reference genome" name="fasta_item" type="select">
1
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105 <options from_data_table="all_fasta">
0
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106 <filter column="2" type="sort_by"/>
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107 </options>
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108 </param>
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109 <expand macro="index_parameter"/>
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110 </when>
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111 </conditional>
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112 <param name="outformat" type="select" label="Produce alignment with softclipping?">
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113 <option value="-osh">Produce alignment with hard clipping</option>
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114 <option value="-oss">Produce alignment with soft clipping</option>
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115 </param>
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116 <param type="integer" argument="-BW" value="5" min="0" label="BandWidth" help="band size on each side of the diagonal of banded Smith Waterman" />
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117 <param type="integer" argument="-G" value="50" min="0" label="maxGap" help="maximum indel size allowed with a single alignment" />
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118 <param type="integer" argument="-H" value="650" min="1" max="65525" label="maxHits" help="maximum times a seed is in the reference before it is ignored as too repetitive. To take advantage of k-mer sampling, use the same value of maxHits during index creation and alignment." />
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119 <param type="integer" argument="-M" value="25" min="0" label="minMatch" help="minimum number of bases in seeds to start an alignment" />
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120 <param type="integer" argument="-MD" value="50" min="0" label="MaxDesert" help="maximum number of contiguous bases without a seed before alignmment is split" />
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121 <param type="float" argument="-P" value="0.9" min="0" label="minPercent-identity" help="minimum matching/alignment-length for a query to be included in output" />
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122 <param type="integer" argument="-X" value="25" min="0" label="Xdropoff" help="maximum score dropoff before terminating alignment extensions" />
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123 <conditional name="ags">
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124 <param name="use_ags" type="select" label="Use Affine Gap Scoring?">
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125 <option value="yes" selected="True">Yes</option>
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126 <option value="no">No</option>
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127 </param>
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128 <when value="yes">
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129 <param argument="-GEC" type="integer" value="2" min="0" label="GapExtensionCost" help="cost for extending a gap (indel)"/>
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130 <param argument="-GOC" type="integer" value="5" min="0" label="GapOpenCost" help="cost for starting a new gap (indel)"/>
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131 <param argument="-MS" type="integer" value="1" min="0" label="MatchScore" help="score added for each matching base"/>
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132 <param argument="-RC" type="integer" value="3" min="0" label="ReplacementCost" help="score subtracted for each mismatched base"/>
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133 </when>
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134 <when value="no">
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135 </when>
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136 </conditional>
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137 <conditional name="oqc">
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138 <param name="use_oqc" type="select" label="Use Optimal Query Coverage Algorithm?" help="">
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139 <option value="yes" selected="True">Yes (Find a set of alignments are found that optimally cover the query, using the remaining options)</option>
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140 <option value="no">No (Output all alignments meeting above criteria)</option>
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141 </param>
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142 <when value="yes">
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143 <param argument="-BP" type="integer" value="5" min="0" label="BreakpointPenalty" help="penalty for inserting a breakpoint in split-read alignment"/>
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144 <param argument="-MGDP" type="integer" value="5" min="0" label="MaxGenomicDistancePenalty"/>
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145 <param argument="-MNO" type="integer" value="25" min="0" label="MinNonOverlap" help="minimum number of unshared bases required in each split alignment"/>
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146 </when>
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147 <when value="no">
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148 </when>
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149 </conditional>
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150 <conditional name="fbs">
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151 <param name="use_fbs" type="select" label="Use Filter By Similarity Algorithm?" help="">
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152 <option value="yes" selected="False">Yes (Output alignments similar to best alignment found using OQC.)</option>
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153 <option value="no">No</option>
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154 </param>
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155 <when value="yes">
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156 <param argument="-PRL" type="float" value="0.9" min="0" max="1" label="PercentReciprocalLength" help="minimum ratio of overlapping length between similar alignment"/>
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157 <param argument="-PSS" type="float" value="0.9" min="0" max="1" label="PercentSimilarScore" help="minimum ratio of scores between similar alignments"/>
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158 </when>
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159 <when value="no">
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160 </when>
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161 </conditional>
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162 </inputs>
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163 <outputs>
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164 <data name="alignment" format="bam" />
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165 </outputs>
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166 <tests>
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167 <test>
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168 <param name="q" value="input.fastq" ftype="fastqsanger"/>
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169 <param name="reference_genome_source" value="history"/>
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170 <param name="history_item" value="phiX.fa" ftype="fasta"/>
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171 <output name="alignment" value="alignment.bam" ftype="bam"/>
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172 </test>
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173 </tests>
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174 <help><![CDATA[
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175 Summary
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176 -------
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177
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178 *yaha* is an open source, flexible, sensitive and accurate DNA aligner
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179 designed for single-end reads. It supports three major modes of
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180 operation:
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181
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182 1. The default “Optimal Query Coverage” (**-OQC**) mode reports the best
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183 set of alignments that cover the length of each query.
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184 2. Using “Filter By Similarity” (**-FBS**), along with the best set of
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185 alignments, *yaha* will also output alignments that are highly
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186 similar to an alignment in the best set.
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187 3. Finally, *yaha* can output all the alignments found for each query.
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188
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189 The **-OQC** and **-FBS** modes are specifically tuned to form split
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190 read mappings that can be used to accurately identify structural
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191 variation events (deletions, duplications, insertions or inversions)
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192 between the subject query and the reference genome.
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193
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194 Usage
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195 -----
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196
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197 **OPTIONS:** Default values enclosed in square brackets []
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198
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199 ::
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200
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201 Input/Output Options:
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202 -g FILE input genome file to use during index creation (FASTA or nib2)
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203 -q FILE input file of sequence reads to align (FASTA or FASTQ) [STDIN]
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204 -osh FILE output file for alignment output in SAM format with hard clipping(default) [STDOUT]
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205 -oss FILE output file for alignment output in SAM format with soft clipping [STDOUT]
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206 -x FILE reference index file to use during alignment
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207 NOTE: At most one of -osh or -oss should be specified.
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208
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209 Index Creation Options:
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210 -H INT maxHits: During index creation, seeds occuring more than maxHits times will be sampled [65565]
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211 -L INT seedLength: Length of seed to use. During alignment, seed length is taken from index file [15]
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212 -S INT Skipdistance: Number of bases to skip ahead before forming next seed [1]
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213
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214 General Alignment Options:
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215 -BW INT BandWidth: band size on each side of the diagonal of banded Smith Waterman [5]
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216 -G INT maxGap: maximum indel size allowed with a single alignment [50]
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217 -H INT maxHits: maximum times a seed is in the reference before it is ignored as too repetitive [650]
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218 -M INT minMatch: minimum number of bases in seeds to start an alignment [25]
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219 -MD INT MaxDesert: maximum number of contiguous bases without a seed before alignmment is split [50]
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220 -P REAL minPercent-identity: minimum matching/alignment-length for a query to be included in output [0.9]
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221 -X INT Xdropoff: maximum score dropoff before terminating alignment extensions [25]
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222 -t INT numThreads: number of threads used to parallel process reads [1]
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223
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224 Affine Gap Scoring Options:
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225 If -AGS is off, a simple edit distance calculation is done.
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226 If on, the remaining options are used:
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227 -AGS BOOL (Y|N) controls use of Affine Gap Scoring [Y].
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228 -GEC INT GapExtensionCost: cost for extending a gap (indel) [2]
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229 -GOC INT GapOpenCost: cost for starting a new gap (indel) [5]
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230 -MS INT MatchScore: score added for each matching base [1]
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231 -RC INT ReplacementCost: score subtracted for each mismatched base [3]
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232
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233 Optimal Query Coverage Options:
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234 If -OQC if off, all alignments meeting above criteria are output.
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235 If -OQC is on, a set of alignments are found that optimally cover the query, using the remaining options.
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236 -OQC BOOL (Y|N) controls use of the Optimal Query Coverage Algorithm.
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237 -BP INT BreakpointPenalty: penalty for inserting a breakpoint in split-read alignment [5]
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238 -MGDP INT MaxGenomicDistancePenalty (5)]
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239 -MNO INT MinNonOverlap: minimum number of unshared bases required in each split alignment [minMatch]
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240 NOTE: The total cost of adding a breakpoint in a split-read mapping is:
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241 BP*MIN(MGDP, Log10(genomic distance between reference loci))
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242
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243 Filter By Similarity Options:
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244 If -FBS is on, the remaining options are used. An alignemnt must satisfy BOTH criteria to be "similar".
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245 -FBS BOOL (Y|N) controls output of alignments similar to best alignment found using OQC.
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246 -PRL REAL PercentReciprocalLength: minimum ratio of overlapping length between similar alignemnt [0.9]
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247 -PSS REAL PercentSimilarScore: minimum ratio of scores between similar alignments [0.9]
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248
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249 See the `User Guide <https://www.dropbox.com/s/7j758vpbaskcq20/YAHA_User_Guide.0.1.83.pdf?dl=0>`__
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250 for more details on all options and their usage.
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251
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252 | **Written by:** Greg Faust (gf4ea@virginia.edu)
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253 | `Ira Hall Lab, University of
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254 Virginia <http://faculty.virginia.edu/irahall/>`__
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255
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256 | **Please cite:**
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257 | `Faust G.G. and Hall I.M., "*YAHA*: fast and flexible long-read
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258 alignment with optimal breakpoint detection," *Bioinformatics* Oct.
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259 2012; **28**\ (19):
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260 2417-2424. <http://bioinformatics.oxfordjournals.org/content/28/19/2417>`__
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261 ]]></help>
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262 <citations>
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263 <citation type="doi">10.1093/bioinformatics/bts456</citation>
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264 </citations>
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265 </tool>