annotate sailfish.xml @ 5:1b4ed566a41c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 03edb751808fef8bce744ebcbad5661a32373211
author bgruening
date Wed, 02 Nov 2016 10:30:36 -0400
parents 03c74355227f
children 5bc9cd008ceb
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5
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1 <tool id="sailfish" name="Sailfish" version="0.10.1">
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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>
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12 <requirements>
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13 <requirement type="package" version="0.10.1">sailfish</requirement>
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14 </requirements>
0
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15 <stdio>
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16 <exit_code range="1:" />
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17 <exit_code range=":-1" />
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18 <regex match="Error:" />
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19 <regex match="Exception:" />
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20 <regex match="Exception :" />
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21 </stdio>
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22 <version_command>sailfish -version</version_command>
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23 <command>
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24 <![CDATA[
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25 #if $refTranscriptSource.TranscriptSource == "history":
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26 sailfish index
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27 --transcripts $refTranscriptSource.ownFile
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28 --kmerSize $refTranscriptSource.kmerSize
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29 --out ./index_dir
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30 --threads "\${GALAXY_SLOTS:-4}"
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31 #set $index_path = './index_dir'
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32 #else:
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33 #set $index_path = $refTranscriptSource.index.fields.path
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34 #end if
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35 &&
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36 #if $single_or_paired.single_or_paired_opts == 'single':
1
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37 #if $single_or_paired.input_singles.ext == 'fasta':
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38 #set $ext = 'fasta'
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39 #else:
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40 #set $ext = 'fastq'
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41 #end if
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42 ln -s $single_or_paired.input_singles ./single.$ext &&
0
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43 #else:
1
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44 #if $single_or_paired.input_mate1.ext == 'fasta':
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45 #set $ext = 'fasta'
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46 #else:
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47 #set $ext = 'fastq'
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48 #end if
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49 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
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50 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
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51 #end if
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52 #if $geneMap:
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53 ln -s "$geneMap" ./geneMap.$geneMap.ext &&
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54 #end if
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55 sailfish quant
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56 --index $index_path
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57 #if $single_or_paired.single_or_paired_opts == 'single':
1
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58 --libType ${single_or_paired.strandedness}
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59 --unmatedReads ./single.$ext
0
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60 #else:
1
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61 --mates1 ./mate1.$ext
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62 --mates2 ./mate2.$ext
0
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63 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
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64 #end if
5
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65 --output ./results
0
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66 $biasCorrect
5
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67 $gcBiasCorrect
0
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68 --threads "\${GALAXY_SLOTS:-4}"
5
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69 $dumpEq
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70 #if str($gcSizeSamp):
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71 --gcSizeSamp $gcSizeSamp
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72 #end if
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73 #if str($gcSpeedSamp):
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74 --gcSpeedSamp $gcSpeedSamp
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75 #end if
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76 #if str($fldMean):
0
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77 --fldMean $fldMean
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78 #end if
5
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79 #if str($fldSD):
0
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80 --fldSD $fldSD
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81 #end if
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82 #if $maxReadOcc:
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83 --maxReadOcc $maxReadOcc
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84 #end if
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85 #if $geneMap:
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86 --geneMap ./geneMap.${geneMap.ext}
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87 #end if
5
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88 $strictIntersect
0
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89 $noEffectiveLengthCorrection
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90 $useVBOpt
5
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91 $discardOrphans
0
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92 $unsmoothedFLD
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93 --maxFragLen ${maxFragLen}
5
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94 --txpAggregationKey '${txpAggregationKey}'
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95 $ignoreLibCompat
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96 $enforceLibCompat
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97 $allowDovetail
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98 #if str($numBiasSamples):
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99 --numBiasSamples $numBiasSamples
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100 #end if
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101 #if str($numFragSamples):
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102 --numFragSamples $numFragSamples
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103 #end if
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104 #if str($numGibbsSamples):
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105 --numGibbsSamples $numGibbsSamples
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106 #end if
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107 #if str($numBootstraps):
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108 --numBootstraps $numBootstraps
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109 #end if
0
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110 ]]>
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111 </command>
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112 <inputs>
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113 <conditional name="refTranscriptSource">
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114 <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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115 <option value="indexed">Use a built-in index</option>
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116 <option value="history" selected="True">Use one from the history</option>
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117 </param>
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118 <when value="indexed">
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119 <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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120 <options from_data_table="sailfish_indexes">
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121 <filter type="sort_by" column="2"/>
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122 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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123 </options>
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124 </param>
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125 </when> <!-- build-in -->
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126 <when value="history">
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127 <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" />
0
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128 <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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129 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors.
0
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130 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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131 the more distinct they will be. We generally recommend using a k-mer size of at least 20."/>
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132 </when> <!-- history -->
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133 </conditional> <!-- refTranscriptSource -->
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134
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135 <conditional name="single_or_paired">
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136 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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137 <option value="single">Single-end</option>
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138 <option value="paired">Paired-end</option>
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139 </param>
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140 <when value="single">
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141 <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
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142 <expand macro="strandedness" />
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143 </when>
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144 <when value="paired">
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145 <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
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146 <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
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147 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
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148 <option value="M">Mates are oriented in the same direction (M = matching)</option>
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149 <option value="O">Mates are oriented away from each other (O = outward)</option>
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150 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
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151 </param>
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152 <expand macro="strandedness" />
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153 </when>
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154 </conditional>
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155
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156 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes"
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157 help="Calculates the aggregated gene-level abundance estimations. This file should be eiher a GTF file or tab-delimited format
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158 where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
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159
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160 <param argument="--biasCorrect" type="boolean" truevalue="--biasCorrect" falsevalue="" checked="False"
5
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161 label="Perform sequence-specific bias correction" help=""/>
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162
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163 <param argument="--gcBiasCorrect" type="boolean" truevalue="--gcBiasCorrect" falsevalue="" checked="False"
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164 label="Perform fragment GC bias correction" help=""/>
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165
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166 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
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167 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
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168
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169 <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
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170 label="The value by which to down-sample transcripts when representing the GC content"
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171 help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>
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172
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173 <param argument="--gcSpeedSamp" type="integer" value="1" optional="True"
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174 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias."
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175 help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
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176
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177 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
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178 label="Strict Intersect." help="When this flag is set, if the intersection of the
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179 quasi-mappings for the left and right is empty, then all mappings for the left and all mappings
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180 for the right read are reported as orphaned quasi-mappings."/>
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181
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182 <param argument="--fldMean" type="integer" value="200" optional="True" label="Calculate effective lengths"
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183 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely
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184 mapping reads when performing paired-end quantification
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185 to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
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186
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187 <param argument="--fldSD" type="integer" value="80" optional="True" label="Standard deviation"
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188 help="The standard deviation used in the fragment length distribution for single-end quantification or
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189 when an empirical distribution cannot be learned."/>
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190
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191 <param argument="--maxReadOcc" type="integer" value="200" optional="True" label="Maximal read mapping occurence"
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192 help="Reads mapping to more than this many places won't be considered."/>
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193
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194 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
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195 label="Disable effective length correction" help="Disables effective length correction when computing the probability
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196 that a fragment was generated from a transcript.
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197 If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
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198
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199 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
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200 label="Use Variational Bayesian EM algorithm for optimization" help="Use Variational Bayesian EM algorithm rather
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201 than the traditional EM angorithm for optimization"/>
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202
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203 <param argument="--discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
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204 label="Discard orphaned reads as valid hits when performing lightweight-alignment"
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205 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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206
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207 <param argument="--unsmoothedFLD" type="boolean" truevalue="--unsmoothedFLD" falsevalue="" checked="False"
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208 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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209 characteristic function over each transcript."/>
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210
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211 <param argument="--maxFragLen" type="integer" value="1000" optional="True"
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212 label="The maximum length of a fragment to consider when building the empirical fragment length distribution"
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213 help=""/>
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214
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215 <param argument="--txpAggregationKey" value="gene_id" type="text" label="The key for aggregating transcripts during gene-level estimates">
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216 <help>
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217 <![CDATA[
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218 When generating the gene-level estimates, use the provided key for aggregating transcripts. The default is the "gene_id" field,
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219 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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220 affects aggregation when using a GTF annotation; not an annotation in "simple" format.]]>
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221 </help>
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222 </param>
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223 <param argument="--ignoreLibCompat" type="boolean" truevalue="--ignoreLibCompat" falsevalue="" checked="False"
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224 label="Disables strand-aware processing completely.">
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225 <help>
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226 <![CDATA[
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227 All hits are considered "Valid".]]>
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228 </help>
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229 </param>
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230 <param argument="--enforceLibCompat" type="boolean" truevalue="--enforceLibCompat" falsevalue="" checked="False"
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231 label="Enforces strict library compatibility.">
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232 <help>
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233 <![CDATA[
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234 Fragments that map in a manner other than what is specified by the expected library type will be discarded,
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235 even if there are no mappings that agree with the expected library type.]]>
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236 </help>
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237 </param>
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238 <param argument="--allowDovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False"
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239 label="Allow paired-end reads from the same fragment to dovetail.">
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240 <help>
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241 <![CDATA[
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242 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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243 </help>
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244 </param>
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245 <param argument="--numBiasSamples" type="integer" value="1000000" optional="True"
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246 label="Number of fragment mappings to use when learning the sequene-specific bias model"
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247 help=""/>
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248 <param argument="--numFragSamples" type="integer" value="10000" optional="True"
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249 label="Number of fragments from unique alignments to sample when building the fragment length distribution"
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250 help=""/>
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251 <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
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252 label="Number of Gibbs sampling rounds to perform."
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253 help=""/>
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254 <param argument="--numBootstraps" type="integer" value="0" optional="True"
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255 label="Number of bootstrap samples to generate."
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256 help="This is mutually exclusive with Gibbs"/>
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257 </inputs>
0
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258
5
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259
0
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260 <outputs>
5
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261 <data name="output_quant" format="tabular" from_work_dir="results/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
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262 <data name="output_gene_quant" format="tabular" from_work_dir="results/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
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263 <filter>geneMap</filter>
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264 </data>
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265 </outputs>
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266 <tests>
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267 <test>
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268 <param name="single_or_paired_opts" value="paired" />
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269 <param name="input_mate1" value="reads_1.fastq" />
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270 <param name="input_mate2" value="reads_2.fastq" />
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271 <param name="biasCorrect" value="False" />
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272 <param name="TranscriptSource" value="history" />
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273 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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274 <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
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275 </test>
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276 <test>
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277 <param name="single_or_paired_opts" value="paired" />
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278 <param name="input_mate1" value="reads_1.fastq" />
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279 <param name="input_mate2" value="reads_2.fastq" />
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280 <param name="biasCorrect" value="True" />
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281 <param name="TranscriptSource" value="history" />
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282 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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283 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
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284 </test>
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285 <test>
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286 <param name="single_or_paired_opts" value="paired" />
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287 <param name="input_mate1" value="reads_1.fastq" />
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288 <param name="input_mate2" value="reads_2.fastq" />
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289 <param name="biasCorrect" value="True" />
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290 <param name="TranscriptSource" value="history" />
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291 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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292 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
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293 <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
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294 <output file="sailfish_genMap_result1.tab" ftype="tabular" name="output_gene_quant" />
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295 </test>
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296 </tests>
5
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297 <help><![CDATA[
4
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298
0
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299 **What it does**
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300
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301 Sailfish is a tool for transcript quantification from RNA-seq data. It
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302 requires a set of target transcripts (either from a reference or de-novo
0
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303 assembly) to quantify. All you need to run Sailfish is a fasta file containing
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304 your reference transcripts and a (set of) fasta/fastq file(s) containing your
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305 reads. Sailfish runs in two phases; indexing and quantification. The indexing
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306 step is independent of the reads, and only need to be run one for a particular
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307 set of reference transcripts and choice of k (the k-mer size). The
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308 quantification step, obviously, is specific to the set of RNA-seq reads and is
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309 thus run more frequently.
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310
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311 When the quantification output contains a number of columns:
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312 (1) Transcript ID,
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313 (2) Transcript Length,
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314 (3) Transcripts per Million (TPM) and
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315 (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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316
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317 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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318 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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319 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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320 (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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321
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322
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323
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324 Fragment Library Types
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325 ======================
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326
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327 There are numerous library preparation protocols for RNA-seq that result in
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328 sequencing reads with different characteristics. For example, reads can be
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329 single end (only one side of a fragment is recorded as a read) or paired-end
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330 (reads are generated from both ends of a fragment). Further, the sequencing
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331 reads themselves may be unstraned or strand-specific. Finally, paired-end
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332 protocols will have a specified relative orientation. To characterize the
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333 various different typs of sequencing libraries, we've created a miniature
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334 "language" that allows for the succinct description of the many different types
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335 of possible fragment libraries. For paired-end reads, the possible
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336 orientations, along with a graphical description of what they mean, are
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337 illustrated below:
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338
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339 .. image:: ReadLibraryIllustration.png
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340
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341 The library type string consists of three parts: the relative orientation of
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342 the reads, the strandedness of the library, and the directionality of the
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343 reads.
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344
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345 The first part of the library string (relative orientation) is only provided if
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346 the library is paired-end. The possible options are:
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347
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348 ::
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349
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350 I = inward
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351 O = outward
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352 M = matching
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353
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354 The second part of the read library string specifies whether the protocol is
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355 stranded or unstranded; the options are:
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356
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357 ::
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358
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359 S = stranded
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360 U = unstranded
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361
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362 If the protocol is unstranded, then we're done. The final part of the library
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363 string specifies the strand from which the read originates in a strand-specific
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364 protocol — it is only provided if the library is stranded (i.e. if the
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365 library format string is of the form S). The possible values are:
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366
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367 ::
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368
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369 F = read 1 (or single-end read) comes from the forward strand
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370 R = read 1 (or single-end read) comes from the reverse strand
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371
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372 So, for example, if you wanted to specify a fragment library of strand-specific
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373 paired-end reads, oriented toward each other, where read 1 comes from the
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374 forward strand and read 2 comes from the reverse strand, you would specify ``-l
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375 ISF`` on the command line. This designates that the library being processed has
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376 the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
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377 (the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
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378 strand).
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379
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380 The single end library strings are a bit simpler than their pair-end counter
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381 parts, since there is no relative orientation of which to speak. Thus, the
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382 only possible library format types for single-end reads are ``U`` (for
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383 unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
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384 and ``SR`` (for strand-specific reads coming from the reverse strand).
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385
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386 A few more examples of some library format strings and their interpretations are:
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387
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388 ::
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389
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390 IU (an unstranded paired-end library where the reads face each other)
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391
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392 ::
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393
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394 SF (a stranded single-end protocol where the reads come from the forward strand)
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395
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396 ::
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397
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398 OSR (a stranded paired-end protocol where the reads face away from each other,
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399 read1 comes from reverse strand and read2 comes from the forward strand)
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400
4
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401 .. note:: Correspondence to TopHat library types
0
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402
4
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403 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
0
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404 read aligner has a different convention for specifying the format of the library.
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405 Below is a table that provides the corresponding sailfish/salmon library format
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406 string for each of the potential TopHat library types:
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407
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408
4
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409 +---------------------+-------------------------+
0
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410 | TopHat | Salmon (and Sailfish) |
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411 +=====================+============+============+
4
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412 | | Paired-end | Single-end |
0
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413 +---------------------+------------+------------+
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414 |``-fr-unstranded`` |``-l IU`` |``-l U`` |
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415 +---------------------+------------+------------+
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416 |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |
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417 +---------------------+------------+------------+
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418 |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |
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419 +---------------------+------------+------------+
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420
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421 The remaining salmon library format strings are not directly expressible in terms
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422 of the TopHat library types, and so there is no direct mapping for them.
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423
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424
5
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425 ]]></help>
1b4ed566a41c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 03edb751808fef8bce744ebcbad5661a32373211
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426 <citations>
1b4ed566a41c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 03edb751808fef8bce744ebcbad5661a32373211
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427 <citation type="doi">10.1038/nbt.2862</citation>
1b4ed566a41c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 03edb751808fef8bce744ebcbad5661a32373211
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428 </citations>
0
3b4ed0e473dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sailfish commit bd2dd2419ea52f30cd7de2f7109a12b49b5d0dba-dirty
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429 </tool>