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annotate sailfish.xml @ 7:a8f343909c17 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 359ddec398e18d3e2a534239b1202691595d1243
author bgruening
date Thu, 13 Apr 2017 09:23:59 -0400
parents 5bc9cd008ceb
children
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6
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1 <tool id="sailfish" name="Sailfish" version="0.10.1.1">
0
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2 <description>transcript quantification from RNA-seq data</description>
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3 <macros>
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4 <xml name="strandedness">
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5 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
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6 <option value="U" selected="True">Not stranded (U)</option>
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7 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
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8 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
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9 </param>
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10 </xml>
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11 </macros>
5
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12 <requirements>
6
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13 <requirement type="package" version="1.0.6">bzip2</requirement>
5
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14 <requirement type="package" version="0.10.1">sailfish</requirement>
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15 </requirements>
0
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16 <stdio>
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17 <exit_code range="1:" />
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18 <exit_code range=":-1" />
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19 <regex match="Error:" />
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20 <regex match="Exception:" />
1
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21 <regex match="Exception :" />
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22 </stdio>
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23 <version_command>sailfish -version</version_command>
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24 <command>
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25 <![CDATA[
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26 #if $refTranscriptSource.TranscriptSource == "history":
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27 sailfish index
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28 --transcripts $refTranscriptSource.ownFile
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29 --kmerSize $refTranscriptSource.kmerSize
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30 --out ./index_dir
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31 --threads "\${GALAXY_SLOTS:-4}"
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32 #set $index_path = './index_dir'
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33 #else:
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34 #set $index_path = $refTranscriptSource.index.fields.path
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35 #end if
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36 &&
6
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37 #set compressed = 'no'
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38 #if $single_or_paired.single_or_paired_opts == 'single':
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39 #if $single_or_paired.input_singles.ext == 'fasta':
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40 #set $ext = 'fasta'
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41 #else:
6
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42 #if $single_or_paired.input_singles.is_of_type("fastq.gz"):
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43 #set compressed = 'GZ'
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44 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2"):
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45 #set compressed = 'BZ2'
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46 #end if
1
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47 #set $ext = 'fastq'
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48 #end if
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49 ln -s $single_or_paired.input_singles ./single.$ext &&
0
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50 #else:
1
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51 #if $single_or_paired.input_mate1.ext == 'fasta':
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52 #set $ext = 'fasta'
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53 #else:
6
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54 #if $single_or_paired.input_mate1.is_of_type("fastq.gz"):
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55 #set compressed = 'GZ'
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56 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2"):
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57 #set compressed = 'BZ2'
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58 #end if
1
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59 #set $ext = 'fastq'
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60 #end if
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61 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
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62 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
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63 #end if
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64 #if $geneMap:
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65 ln -s "$geneMap" ./geneMap.$geneMap.ext &&
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66 #end if
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67 sailfish quant
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68 --index $index_path
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69 #if $single_or_paired.single_or_paired_opts == 'single':
1
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70 --libType ${single_or_paired.strandedness}
6
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71 #if $compressed == 'GZ':
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72 --unmatedReads <(zcat ./single.$ext)
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73 #else if $compressed == 'BZ2':
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74 --unmatedReads <(bzcat ./single.$ext)
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75 #else:
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76 --unmatedReads ./single.$ext
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77 #end if
0
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78 #else:
6
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79 #if $compressed == 'GZ':
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80 --mates1 <(zcat ./mate1.$ext)
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81 --mates2 <(zcat ./mate2.$ext)
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82 #else if $compressed == 'BZ2':
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83 --mates1 <(bzcat ./mate1.$ext)
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84 --mates2 <(bzcat ./mate2.$ext)
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85 #else:
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86 --mates1 ./mate1.$ext
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87 --mates2 ./mate2.$ext
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88 #end if
0
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89 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
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90 #end if
5
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91 --output ./results
0
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92 $biasCorrect
5
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93 $gcBiasCorrect
0
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94 --threads "\${GALAXY_SLOTS:-4}"
5
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95 $dumpEq
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96 #if str($gcSizeSamp):
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97 --gcSizeSamp $gcSizeSamp
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98 #end if
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99 #if str($gcSpeedSamp):
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100 --gcSpeedSamp $gcSpeedSamp
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101 #end if
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102 #if str($fldMean):
0
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103 --fldMean $fldMean
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104 #end if
5
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105 #if str($fldSD):
0
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106 --fldSD $fldSD
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107 #end if
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108 #if $maxReadOcc:
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109 --maxReadOcc $maxReadOcc
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110 #end if
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111 #if $geneMap:
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112 --geneMap ./geneMap.${geneMap.ext}
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113 #end if
5
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114 $strictIntersect
0
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115 $noEffectiveLengthCorrection
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116 $useVBOpt
5
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117 $discardOrphans
0
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118 $unsmoothedFLD
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119 --maxFragLen ${maxFragLen}
5
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120 --txpAggregationKey '${txpAggregationKey}'
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121 $ignoreLibCompat
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122 $enforceLibCompat
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123 $allowDovetail
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124 #if str($numBiasSamples):
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125 --numBiasSamples $numBiasSamples
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126 #end if
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127 #if str($numFragSamples):
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128 --numFragSamples $numFragSamples
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129 #end if
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130 #if str($numGibbsSamples):
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131 --numGibbsSamples $numGibbsSamples
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132 #end if
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133 #if str($numBootstraps):
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134 --numBootstraps $numBootstraps
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135 #end if
0
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136 ]]>
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137 </command>
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138 <inputs>
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139 <conditional name="refTranscriptSource">
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140 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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141 <option value="indexed">Use a built-in index</option>
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142 <option value="history" selected="True">Use one from the history</option>
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143 </param>
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144 <when value="indexed">
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145 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
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146 <options from_data_table="sailfish_indexes">
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147 <filter type="sort_by" column="2"/>
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148 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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149 </options>
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150 </param>
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151 </when> <!-- build-in -->
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152 <when value="history">
5
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153 <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" />
0
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154 <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built"
4
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155 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors.
0
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156 The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers,
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157 the more distinct they will be. We generally recommend using a k-mer size of at least 20."/>
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158 </when> <!-- history -->
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159 </conditional> <!-- refTranscriptSource -->
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160
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161 <conditional name="single_or_paired">
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162 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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163 <option value="single">Single-end</option>
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164 <option value="paired">Paired-end</option>
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165 </param>
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166 <when value="single">
6
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167 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." />
0
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168 <expand macro="strandedness" />
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169 </when>
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170 <when value="paired">
6
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171 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." />
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172 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." />
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173 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
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174 <option value="M">Mates are oriented in the same direction (M = matching)</option>
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175 <option value="O">Mates are oriented away from each other (O = outward)</option>
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176 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
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177 </param>
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178 <expand macro="strandedness" />
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179 </when>
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180 </conditional>
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181
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182 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes"
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183 help="Calculates the aggregated gene-level abundance estimations. This file should be eiher a GTF file or tab-delimited format
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184 where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
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185
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186 <param argument="--biasCorrect" type="boolean" truevalue="--biasCorrect" falsevalue="" checked="False"
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187 label="Perform sequence-specific bias correction" help=""/>
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188
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189 <param argument="--gcBiasCorrect" type="boolean" truevalue="--gcBiasCorrect" falsevalue="" checked="False"
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190 label="Perform fragment GC bias correction" help=""/>
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191
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192 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
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193 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
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194
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195 <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
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196 label="The value by which to down-sample transcripts when representing the GC content"
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197 help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>
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198
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199 <param argument="--gcSpeedSamp" type="integer" value="1" optional="True"
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200 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias."
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201 help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
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202
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203 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
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204 label="Strict Intersect." help="When this flag is set, if the intersection of the
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205 quasi-mappings for the left and right is empty, then all mappings for the left and all mappings
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206 for the right read are reported as orphaned quasi-mappings."/>
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207
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208 <param argument="--fldMean" type="integer" value="200" optional="True" label="Calculate effective lengths"
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209 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely
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210 mapping reads when performing paired-end quantification
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211 to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
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212
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213 <param argument="--fldSD" type="integer" value="80" optional="True" label="Standard deviation"
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214 help="The standard deviation used in the fragment length distribution for single-end quantification or
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215 when an empirical distribution cannot be learned."/>
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216
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217 <param argument="--maxReadOcc" type="integer" value="200" optional="True" label="Maximal read mapping occurence"
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218 help="Reads mapping to more than this many places won't be considered."/>
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219
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220 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
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221 label="Disable effective length correction" help="Disables effective length correction when computing the probability
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222 that a fragment was generated from a transcript.
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223 If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
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224
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225 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
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226 label="Use Variational Bayesian EM algorithm for optimization" help="Use Variational Bayesian EM algorithm rather
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227 than the traditional EM angorithm for optimization"/>
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228
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229 <param argument="--discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
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230 label="Discard orphaned reads as valid hits when performing lightweight-alignment"
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231 help="This option will discard orphaned fragments. This only has an effect on paired-end input, but enabling this option will discard, rather than count, any reads where only one of the paired fragments maps to a transcript."/>
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232
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233 <param argument="--unsmoothedFLD" type="boolean" truevalue="--unsmoothedFLD" falsevalue="" checked="False"
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234 label="Use the un-smoothed approach to effective length correction" help="This traditional approach works by convolving the FLD with the
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235 characteristic function over each transcript."/>
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236
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237 <param argument="--maxFragLen" type="integer" value="1000" optional="True"
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238 label="The maximum length of a fragment to consider when building the empirical fragment length distribution"
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239 help=""/>
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240
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241 <param argument="--txpAggregationKey" value="gene_id" type="text" label="The key for aggregating transcripts during gene-level estimates">
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242 <help>
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243 <![CDATA[
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244 When generating the gene-level estimates, use the provided key for aggregating transcripts. The default is the "gene_id" field,
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245 but other fields (e.g. "gene_name") might be useful depending on the specifics of the annotation being used. Note: this option only
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246 affects aggregation when using a GTF annotation; not an annotation in "simple" format.]]>
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247 </help>
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248 </param>
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249 <param argument="--ignoreLibCompat" type="boolean" truevalue="--ignoreLibCompat" falsevalue="" checked="False"
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250 label="Disables strand-aware processing completely.">
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251 <help>
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252 <![CDATA[
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253 All hits are considered "Valid".]]>
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254 </help>
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255 </param>
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256 <param argument="--enforceLibCompat" type="boolean" truevalue="--enforceLibCompat" falsevalue="" checked="False"
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257 label="Enforces strict library compatibility.">
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258 <help>
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259 <![CDATA[
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260 Fragments that map in a manner other than what is specified by the expected library type will be discarded,
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261 even if there are no mappings that agree with the expected library type.]]>
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262 </help>
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263 </param>
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264 <param argument="--allowDovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False"
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265 label="Allow paired-end reads from the same fragment to dovetail.">
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266 <help>
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267 <![CDATA[
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268 Allow paired-end reads from the same fragment to "dovetail", such that the ends of the mapped reads can extend past each other.]]>
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269 </help>
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270 </param>
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271 <param argument="--numBiasSamples" type="integer" value="1000000" optional="True"
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272 label="Number of fragment mappings to use when learning the sequene-specific bias model"
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273 help=""/>
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274 <param argument="--numFragSamples" type="integer" value="10000" optional="True"
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275 label="Number of fragments from unique alignments to sample when building the fragment length distribution"
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276 help=""/>
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277 <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
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278 label="Number of Gibbs sampling rounds to perform."
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279 help=""/>
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280 <param argument="--numBootstraps" type="integer" value="0" optional="True"
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281 label="Number of bootstrap samples to generate."
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282 help="This is mutually exclusive with Gibbs"/>
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283 </inputs>
0
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284
5
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285
0
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286 <outputs>
5
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287 <data name="output_quant" format="tabular" from_work_dir="results/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
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288 <data name="output_gene_quant" format="tabular" from_work_dir="results/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
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289 <filter>geneMap</filter>
0
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290 </data>
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291 </outputs>
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292 <tests>
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293 <test>
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294 <param name="single_or_paired_opts" value="paired" />
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295 <param name="input_mate1" value="reads_1.fastq" />
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296 <param name="input_mate2" value="reads_2.fastq" />
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297 <param name="biasCorrect" value="False" />
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298 <param name="TranscriptSource" value="history" />
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299 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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300 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
5
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301 </test>
6
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302 <test> <!-- gzipped version of above -->
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303 <param name="single_or_paired_opts" value="paired" />
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304 <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
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305 <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
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306 <param name="biasCorrect" value="False" />
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307 <param name="TranscriptSource" value="history" />
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308 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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309 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
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310 </test>
5
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311 <test>
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312 <param name="single_or_paired_opts" value="paired" />
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313 <param name="input_mate1" value="reads_1.fastq" />
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314 <param name="input_mate2" value="reads_2.fastq" />
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315 <param name="biasCorrect" value="True" />
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316 <param name="TranscriptSource" value="history" />
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317 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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318 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
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319 </test>
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320 <test>
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321 <param name="single_or_paired_opts" value="paired" />
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322 <param name="input_mate1" value="reads_1.fastq" />
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323 <param name="input_mate2" value="reads_2.fastq" />
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324 <param name="biasCorrect" value="True" />
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325 <param name="TranscriptSource" value="history" />
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326 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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327 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
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328 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
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329 <output file="sailfish_genMap_result1.tab" ftype="tabular" name="output_gene_quant" />
0
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330 </test>
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331 </tests>
5
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332 <help><![CDATA[
4
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333
0
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334 **What it does**
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335
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336 Sailfish is a tool for transcript quantification from RNA-seq data. It
2
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337 requires a set of target transcripts (either from a reference or de-novo
0
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338 assembly) to quantify. All you need to run Sailfish is a fasta file containing
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339 your reference transcripts and a (set of) fasta/fastq file(s) containing your
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340 reads. Sailfish runs in two phases; indexing and quantification. The indexing
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341 step is independent of the reads, and only need to be run one for a particular
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342 set of reference transcripts and choice of k (the k-mer size). The
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343 quantification step, obviously, is specific to the set of RNA-seq reads and is
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344 thus run more frequently.
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345
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346 When the quantification output contains a number of columns:
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347 (1) Transcript ID,
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348 (2) Transcript Length,
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349 (3) Transcripts per Million (TPM) and
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350 (4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).
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351
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352 The first two columns are self-explanatory, the next four are measures of transcript abundance and the final is a commonly used input for differential expression tools.
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353 The Transcripts per Million quantification number is computed as described in [1], and is meant as an estimate of the number of transcripts, per million observed transcripts,
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354 originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
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355 (i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).
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356
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357
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358
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359 Fragment Library Types
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360 ======================
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361
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362 There are numerous library preparation protocols for RNA-seq that result in
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363 sequencing reads with different characteristics. For example, reads can be
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364 single end (only one side of a fragment is recorded as a read) or paired-end
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365 (reads are generated from both ends of a fragment). Further, the sequencing
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366 reads themselves may be unstraned or strand-specific. Finally, paired-end
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367 protocols will have a specified relative orientation. To characterize the
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368 various different typs of sequencing libraries, we've created a miniature
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369 "language" that allows for the succinct description of the many different types
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370 of possible fragment libraries. For paired-end reads, the possible
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371 orientations, along with a graphical description of what they mean, are
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372 illustrated below:
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373
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374 .. image:: ReadLibraryIllustration.png
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375
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376 The library type string consists of three parts: the relative orientation of
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377 the reads, the strandedness of the library, and the directionality of the
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378 reads.
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379
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380 The first part of the library string (relative orientation) is only provided if
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381 the library is paired-end. The possible options are:
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382
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383 ::
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384
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385 I = inward
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386 O = outward
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387 M = matching
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388
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389 The second part of the read library string specifies whether the protocol is
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390 stranded or unstranded; the options are:
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391
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392 ::
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393
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394 S = stranded
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395 U = unstranded
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396
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397 If the protocol is unstranded, then we're done. The final part of the library
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398 string specifies the strand from which the read originates in a strand-specific
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399 protocol — it is only provided if the library is stranded (i.e. if the
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400 library format string is of the form S). The possible values are:
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401
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402 ::
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403
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404 F = read 1 (or single-end read) comes from the forward strand
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405 R = read 1 (or single-end read) comes from the reverse strand
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406
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407 So, for example, if you wanted to specify a fragment library of strand-specific
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408 paired-end reads, oriented toward each other, where read 1 comes from the
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409 forward strand and read 2 comes from the reverse strand, you would specify ``-l
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410 ISF`` on the command line. This designates that the library being processed has
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411 the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
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412 (the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
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413 strand).
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414
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415 The single end library strings are a bit simpler than their pair-end counter
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416 parts, since there is no relative orientation of which to speak. Thus, the
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417 only possible library format types for single-end reads are ``U`` (for
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418 unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
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419 and ``SR`` (for strand-specific reads coming from the reverse strand).
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420
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421 A few more examples of some library format strings and their interpretations are:
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422
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423 ::
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424
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425 IU (an unstranded paired-end library where the reads face each other)
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426
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427 ::
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428
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429 SF (a stranded single-end protocol where the reads come from the forward strand)
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430
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431 ::
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432
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433 OSR (a stranded paired-end protocol where the reads face away from each other,
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434 read1 comes from reverse strand and read2 comes from the forward strand)
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435
4
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436 .. note:: Correspondence to TopHat library types
0
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437
4
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438 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
0
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439 read aligner has a different convention for specifying the format of the library.
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440 Below is a table that provides the corresponding sailfish/salmon library format
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441 string for each of the potential TopHat library types:
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442
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443
4
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444 +---------------------+-------------------------+
0
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445 | TopHat | Salmon (and Sailfish) |
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446 +=====================+============+============+
4
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447 | | Paired-end | Single-end |
0
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448 +---------------------+------------+------------+
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449 |``-fr-unstranded`` |``-l IU`` |``-l U`` |
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450 +---------------------+------------+------------+
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451 |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |
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452 +---------------------+------------+------------+
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453 |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |
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454 +---------------------+------------+------------+
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455
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456 The remaining salmon library format strings are not directly expressible in terms
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457 of the TopHat library types, and so there is no direct mapping for them.
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458
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459
5
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460 ]]></help>
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461 <citations>
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462 <citation type="doi">10.1038/nbt.2862</citation>
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463 </citations>
0
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464 </tool>