Mercurial > repos > shians > shrnaseq

annotate hairpinTool.xml @ 18:11777fbeac32 default tip

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Requirements temporarily removed
author shian_su <registertonysu@gmail.com>
date Wed, 17 Feb 2016 11:15:12 +1100
parents 438f2733bc27
children
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1 <tool id="shRNAseq" name="shRNAseq Tool" version="1.2.1">
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2 <description>
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3 Analyse differential representation for shRNAseq and sgRNA based procedures
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4 using edgeR package from Bioconductor.
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5 </description>
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6
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7 <requirements>
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8 <!-- <requirement type="R-module" version="3.7.17">edgeR</requirement>
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9 <requirement type="R-module" version="3.21.16">limma</requirement>
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10 <requirement type="package" version="3.1.1">R_3_0_3</requirement> -->
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11 <!-- Requirements removed until dependencies properly implemented -->
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12 </requirements>
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13
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14 <stdio>
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15 <exit_code range="1:" level="fatal" description="Tool exception" />
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16 </stdio>
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18 <command interpreter="Rscript">
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19 hairpinTool.R $inputOpt.inputType
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20 #if $inputOpt.inputType=="fastq":
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21
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22 #for $i, $fas in enumerate($inputOpt.fastq):
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23 fastq::$fas.file
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24 #end for
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25
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26 $inputOpt.hairpin
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27 $inputOpt.samples
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28
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29 #if $inputOpt.positions.posOption=="yes":
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30 $inputOpt.positions.barstart
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31 $inputOpt.positions.barend
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32 0
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33 0
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34 $inputOpt.positions.hpstart
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35 $inputOpt.positions.hpend
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36 #else:
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37 1
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42 57
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43 #end if
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44 #elif $inputOpt.inputType=="pairedFastq":
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45
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46 #for $i, $fas in enumerate($inputOpt.fastq):
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47 fastq::$fas.file
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48 #end for
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49
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50 #for $i, $fas in enumerate($inputOpt.fastq):
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51 fastqRev::$fas.fileRev
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52 #end for
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53
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54 $inputOpt.hairpin
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55 $inputOpt.samples
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56
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57 #if $inputOpt.positions.posOption=="yes":
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58 $inputOpt.positions.barstart
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59 $inputOpt.positions.barend
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60 $inputOpt.positions.barstartRev
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61 $inputOpt.positions.barendRev
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62 $inputOpt.positions.hpstart
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63 $inputOpt.positions.hpend
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64 #else:
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65 1
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66 5
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68 0
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70 57
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71 #end if
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72
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73 #elif $inputOpt.inputType=="counts":
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74 $inputOpt.counts
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75 $inputOpt.hairpin
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76 $inputOpt.samples
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77 0
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81 0
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82 #end if
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84 #if $inputOpt.secondaryFactor.secFactorOpt=="yes":
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85 "$inputOpt.secondaryFactor.secFactName"
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86 #else:
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87 "none"
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88 #end if
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89
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90 #if $filterCPM.filtOption=="yes":
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91 $filterCPM.cpmReq
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92 $filterCPM.sampleReq
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93 $filterCPM.readReq
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94 #else:
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95 -Inf
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96 -Inf
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97 -Inf
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98 #end if
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99
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100 "$fdr"
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101 "$lfc"
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102 "$direction"
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103 "$workMode.mode"
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104 "$outFile"
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105 "$outFile.files_path"
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106
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107 #if $workMode.mode=="classic":
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108 "$workMode.pair1"
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109 "$workMode.pair2"
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110 #elif $workMode.mode=="glm":
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111 "$workMode.contrast"
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112 "$workMode.roast.roastOption"
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113
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114 #if $workMode.roast.roastOption=="yes":
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115 "$workMode.roast.hairpinReq"
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116 "$workMode.roast.select.selOption"
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117 "$workMode.roast.select.selection"
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118 #else:
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119 0
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120 0
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121 0
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122 #end if
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123
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124 #end if
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125 </command>
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126
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127 <inputs>
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128 <conditional name="inputOpt">
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129
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130 <param name="inputType" type="select" label="Input File Type">
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131 <option value="fastq">FastQ File</option>
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132 <option value="pairedFastq">Paired FastQ File</option>
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133 <option value="counts">Table of Counts</option>
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134 </param>
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135
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136 <when value="fastq">
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137 <param name="hairpin" type="data" format="tabular"
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138 label="Target Annotation"/>
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139
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140 <param name="samples" type="data" format="tabular"
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141 label="Sample Annotation"/>
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142
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143 <repeat name="fastq" title="FastQ Files">
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144 <param name="file" type="data" format="fastq"/>
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145 </repeat>
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146
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147 <conditional name="secondaryFactor">
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148
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149 <param name="secFactorOpt" type="select"
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150 label="Include Secondary Factor">
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151
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152 <option value="no" selected="True">No</option>
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153
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154 <option value="yes">Yes</option>
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155
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156 </param>
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157
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158 <when value="yes">
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159
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160 <param name="secFactName" type="text" label="Secondary Factor Name"
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161 size="80"/>
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162
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163 </when>
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164
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165 <when value="no">
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166 </when>
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167 </conditional>
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168
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169 <conditional name="positions">
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170 <param name="posOption" type="select"
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171 label="Specify Sample Index and Target Sequence Locations?"
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172 help="Default Positions: Index: 1 to 5, Target: 37 to 57.">
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173 <option value="no" selected="True">No</option>
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174 <option value="yes">Yes</option>
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175 </param>
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176
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177 <when value="yes">
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178 <param name="barstart" type="integer" value="1"
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179 label="Index Starting Position"/>
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180 <param name="barend" type="integer" value="5"
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181 label="Index Ending Position"/>
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182
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183 <param name="hpstart" type="integer" value="37"
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184 label="Target Starting Position"/>
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185
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186 <param name="hpend" type="integer" value="57"
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187 label="Target Ending Position"/>
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188 </when>
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189
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190 <when value="no"/>
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191 </conditional>
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192 </when>
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193
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194 <when value="pairedFastq">
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195 <param name="hairpin" type="data" format="tabular"
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196 label="Target Sequence Annotation"/>
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197
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198 <param name="samples" type="data" format="tabular"
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199 label="Sample Annotation"/>
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200
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201 <repeat name="fastq" title="FastQ Files">
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202 <param name="file" type="data" format="fastq"/>
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203 <param name="fileRev" type="data" format="fastq"/>
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204 </repeat>
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205
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206 <conditional name="secondaryFactor">
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207
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208 <param name="secFactorOpt" type="select"
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209 label="Include Secondary Factor">
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210
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211 <option value="no" selected="True">No</option>
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212
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213 <option value="yes">Yes</option>
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214
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215 </param>
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216
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217 <when value="yes">
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218
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219 <param name="secFactName" type="text" label="Secondary Factor Name"
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220 size="80"/>
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221
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222 </when>
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223
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224 <when value="no">
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225 </when>
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226 </conditional>
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227
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228 <conditional name="positions">
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229
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230 <param name="posOption" type="select"
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231 label="Specify Sample Index and Target Sequence Locations?"
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232 help="Default Positions: Index: 1 to 5, Input required for
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233 reverse end, Target: 37 to 57.">
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234
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235 <option value="no" selected="True">No</option>
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236
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237 <option value="yes">Yes</option>
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238
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239 </param>
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240
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241 <when value="yes">
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242 <param name="barstart" type="integer" value="1"
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243 label="Index Starting Position"/>
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244
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245 <param name="barend" type="integer" value="5"
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246 label="Index Ending Position"/>
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247
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248 <param name="barstartRev" type="integer" value="0"
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249 label="Reverse Index Starting Position"/>
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250
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251 <param name="barendRev" type="integer" value="0"
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252 label="Reverse Index Ending Position"/>
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253
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254 <param name="hpstart" type="integer" value="37"
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255 label="Target Starting Position"/>
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256
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257 <param name="hpend" type="integer" value="57"
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258 label="Target Ending Position"/>
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259 </when>
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260
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261 <when value="no">
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262 </when>
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263
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264 </conditional>
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265
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266 </when>
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267
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268 <when value="counts">
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269
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270 <param name="counts" type="data" format="tabular" label="Counts Table"/>
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271
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272 <param name="hairpin" type="data" format="tabular"
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273 label="Target Sequence Annotation"/>
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274
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275 <param name="samples" type="data" format="tabular"
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276 label="Sample Annotation"/>
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277
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278 <conditional name="secondaryFactor">
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279
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280 <param name="secFactorOpt" type="select"
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281 label="Include Secondary Factor">
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282
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283 <option value="no" selected="True">No</option>
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284
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285 <option value="yes">Yes</option>
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286
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287 </param>
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288
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289 <when value="yes">
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290
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291 <param name="secFactName" type="text" label="Secondary Factor Name"
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292 size="80"/>
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293
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294 </when>
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295
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296 <when value="no">
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297 </when>
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298
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299 </conditional>
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300
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301 </when>
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302
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303 </conditional>
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304
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305 <conditional name="filterCPM">
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306 <param name="filtOption" type="select" label="Filter Low CPM?"
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307 help="Ignore target sequences with very low representation when
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308 performing analysis.">
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309 <option value="yes">Yes</option>
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310 <option value="no">No</option>
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311 </param>
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312
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313 <when value="yes">
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314 <param name="cpmReq" type="float" value="0.5" min="0"
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315 label="Minimum CPM"/>
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316
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317 <param name="sampleReq" type="integer" value="1" min="0"
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318 label="Minimum Samples"
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319 help="Filter out all the genes that do not meet the minimum
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320 CPM in at least this many samples."/>
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321
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322 <param name="readReq" type="integer" value="1000" min="0"
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323 label="Minimum Reads"
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324 help="Filter out all samples that do not have the minimum
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325 number of reads."/>
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326
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327 </when>
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328
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329 <when value="no"/>
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330
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331 </conditional>
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332
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333 <conditional name="workMode">
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334 <param name="mode" type="select" label="Analysis Type"
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335 help="Classic Exact Tests are useful for simple comparisons across
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336 two sampling groups. Generalised linear models allow for more
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337 complex contrasts and gene level analysis to be made.">
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338 <option value="classic">Classic Exact Test</option>
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339 <option value="glm">Generalised Linear Model</option>
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340 </param>
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341
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342 <when value="classic">
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343 <param name="pair1" type="text" label="Compare" size="40"/>
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344 <param name="pair2" type="text" label="To" size="40"
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345 help="The analysis will subtract values of this group from those
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346 in the group above to establish the difference."/>
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347 </when>
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348
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349 <when value="glm">
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350 <param name="contrast" type="text" size="60"
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351 label="Contrasts of interest"
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352 help="Specify equations defining contrasts to be made. Eg.
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353 KD-Control will result in positive fold change if KD has
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354 greater expression and negative if Control has greater
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355 expression."/>
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356
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357 <conditional name="roast">
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358 <param name="roastOption" type="select"
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359 label="Perform Gene Level Analysis?"
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360 help="Analyse LogFC tendencies for target sequences belonging
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361 to the same gene. NOTE: this is a slow procedure that
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362 scales badly with the number of genes analysed.">
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363 <option value="no">No</option>
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364 <option value="yes">Yes</option>
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365 </param>
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366
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367 <when value="yes">
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368 <param name="hairpinReq" type="integer" value="2" min="2"
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369 label="Minimum Targets Found"
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370 help="Only genes with at least this many target sequences
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371 found will be analysed."/>
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372
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373 <conditional name="select">
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374 <param name="selOption" type="select"
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375 label="Gene Selection Method">
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376 <option value="rank">By p-value Rank</option>
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377 <option value="geneID">By Gene Identifier</option>
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378 </param>
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379 <when value="rank">
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380 <param name="selection" type="text" size="40" value="1:5"
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381 label="Ranks of Top Genes to Plot"
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382 help="Genes are ranked in ascending p-value for
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383 differential representation, individual ranks can
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384 be entered seperated by comma or a range seperated
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385 by colon."/>
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386 </when>
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387 <when value="geneID">
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388 <param name="selection" type="text" size="80" value=""
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389 label="Symbols of Genes to Plot"
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390 help="Select genes based on their identifier in the
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391 'Gene' column of the sample information file.
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392 Please ensure exact match with the values in input
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393 file and separate selections with commas."/>
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394 </when>
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395 </conditional>
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396
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397
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398 </when>
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399
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400 <when value="no"/>
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401 </conditional>
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402 </when>
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403 </conditional>
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404
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405 <param name="fdr" type="float" value="0.05" min="0" max="1"
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406 label="FDR Threshold"
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407 help="All observations below this threshold will be highlighted
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408 in the smear plot."/>
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409
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410 <param name="lfc" type="float" value="0" min="0"
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411 label="Absolute LogFC Threshold"
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412 help="In additional to meeting the FDR requirement, the absolute
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413 value of the log-fold-change of the observation must be above
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414 this threshold to be highlighted."/>
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415
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416 <param name="direction" type="select" label="Highlight Option"
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417 help="Only hightlight positive or negative fold changes in smear plot?">
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418 <option value="all">Default</option>
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419 <option value="up">Positive Only</option>
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420 <option value="down">Negative Only</option>
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421 </param>
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422 </inputs>
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423
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424 <outputs>
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425 <data format="html" name="outFile" label="TagSeq Analysis"/>
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426 </outputs>
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427 <help>
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428 .. class:: infomark
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429
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430 **What it does**
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431
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432 Given tables containing information about the hairpins/sgRNA and their
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433 associated sample indices, information about the samples and fastq file
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434 containing the sequencing reads. This tool will generate plots and tables for
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435 the analysis of differential representation.
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436
7
91e411fcdecc Version 1.0.8
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437 .. class:: infomark
91e411fcdecc Version 1.0.8
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438
91e411fcdecc Version 1.0.8
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439 A tutorial of how to use this tool is available at:
91e411fcdecc Version 1.0.8
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440 http://bioinf.wehi.edu.au/shRNAseq/galaxy.html
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441
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442 -----
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443
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444 .. class:: infomark
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445
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446 **INPUTS**
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447
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448 **Input File Type:**
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449
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450 This tool is able to either generate counts from a raw FastQ file given the
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451 information regarding the samples and hairpins/sgRNA. Alternatively if a table
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452 of counts has already been generated it can also be used.
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453
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454 **Counts Table (Counts Input):**
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455
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456 A tab delimited text table of information regarding the counts of
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457 hairpins/sgRNA. Should have a column 'ID' to denote the hairpins/sgRNA that
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458 counts correspond to. Each additional column should have titles corresponding to
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459 the label for the sample.
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460
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461 Example::
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462
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463 ID Sample1 Sample2 Sample3
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464 Control1 49802 48014 40148
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465 Control2 12441 16352 14232
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466 Control3 9842 9148 9111
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467 Hairpin1 3300 3418 2914
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468 Hairpin2 91418 95812 93174
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469 Hairpin3 32985 31975 35104
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470 Hairpin4 12082 14081 14981
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471 Hairpin5 2491 2769 2691
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472 Hairpin6 1294 1486 1642
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473 Hairpin7 49501 49076 47611
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474 ...
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475
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476 **Target Sequence Annotation:**
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477
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478 A tab delimited text table of information regarding the targetted
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479 hairpins/sgRNA sequence. Should have columns 'ID', 'Sequences' and 'Gene' to
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480 uniquely identify the target, align it with the reads to produce counts and
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481 identify which gene the target acts on.
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482
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483 NOTE: the column names are case sensitive and should be input exactly as they
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484 are shown here.
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485
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486 Example::
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487
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488 ID Sequences Gene
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489 Control1 TCTCGCTTGGGCGAGAGTAAG 2
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490 Control2 CCGCCTGAAGTCTCTGATTAA 2
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491 Control3 AGGAATTATAATGCTTATCTA 2
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492 Hairpin1 AAGGCAGAGACTGACCACCTA 4
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493 Hairpin2 GAGCGACCTGGTGTTACTCTA 4
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494 Hairpin3 ATGGTGTAAATAGAGCTGTTA 4
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495 Hairpin4 CAGCTCATCTTCTGTGAAGAA 4
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496 Hairpin5 CAGCTCTGTGGGTCAGAAGAA 4
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497 Hairpin6 CCAGGCACAGATCTCAAGATA 4
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498 Hairpin7 ATGACAAGAAAGACATCTCAA 7
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499 ...
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500
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501 **Sample Annotation (FastQ Input):**
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502
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503 A tab delimited text table of information regarding the samples. Should have
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504 columns 'ID', 'Sequences' and 'group' to uniquely identify each sample, identify
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505 the sample in the reads by its sample index sequence and correctly group
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506 replicates for analysis. Additional columns may inserted for annotation purposes
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507 and will not interfere with analysis as long as the necessary columns are
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508 present.
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509
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510 NOTE: With the exception of other_group, column names are case sensitive and
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511 should be input exactly as they are shown here. The other_group column can be
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512 named by the user and specified in the "Include Secondary Factor" option of the
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513 tool.
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514
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515 Example::
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516
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517 ID Sequences group other_group Replicate
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518 3 GAAAG Day 2 male 1
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519 6 GAACC Day 10 female 1
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520 9 GAAGA Day 5 GFP neg male 1
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521 16 GAATT Day 5 GFP pos male 1
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522 18 GACAC Day 2 female 2
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523 21 GACCA Day 10 male 2
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524 28 GACGT Day 5 GFP neg male 2
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525 31 GACTG Day 5 GFP pos female 2
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526 33 GAGAA Day 2 male 3
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527 40 GAGCT Day 10 female 3
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528 ...
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529
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530 **Include Secondary Factor**
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531 If there are two factors involved in the experiment (i.e. Age and Gender) then
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532 then secondary factor should be included to improve the statistical analysis.
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533 The secondary factor should be specified as a column in the sample annotation
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534 file and the corresponding column name should be input exactly as it is into
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535 the provided field in the tool.
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536
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537 NOTE: Currently the secondary factor is used only to improve statistical
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538 analysis, comparisons can only be made in the primary factor specified as
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539 "group" in the sample annotation.
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540
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541 **Specify Sample Index and Target Sequence Locations (FastQ Input):**
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542
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543 It is assumed that in the sequencing reads that the first 5 bases are the
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544 sample index sequence and that bases 37-57 are the hairpins/sgRNA. If this is
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545 not the case then the values of the positions can be changed, however it still
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546 requires the sample indices and hairpins/sgRNA to be in a consistent location an
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547 in a continuous sequence.
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548
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549 NOTE: position values start at 1 for the first base.
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550
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551 **Filter Low CPM?:**
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552
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553 Often in a large screen there may members with very low counts which are of no
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554 interest in the experiment, these may be filtered out to speed up computations.
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555 Filtering will be based on counts per million in a required number of samples.
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556
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557 **Analysis Type:**
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558
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559 * **Classic Exact Test:** This allows two experimental groups to be compared
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560 and p-values for differential representation derivec for each target
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561 sequence. Simple and fast for straightforward comparisons. In this option you
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562 will have the option of "*Compare* x *To* y" which implicitly subtracts the
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563 data from y from that of x to produce the comparison.
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564
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565 * **Generalised Linear Model:** This allow for complex contrasts to be specified
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566 and also gene level analysis to be performed. If this option is chosen then
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567 contrasts must be explicitly stated in equations and multiple contrasts can
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568 be made. In addition there will be the option to analyse hairpins/sgRNA on a
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569 per-gene basis to see if hairpins/sgRNA belonging to a particular gene have
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570 any overall tendencies for the direction of their log-fold-change.
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571
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572 **FDR Threshold:**
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573 The smear plot in the output will have hairpins/sgRNA highlighted to signify
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574 significant differential representation. The significance is determined by
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575 contorlling the false discovery rate, only those with a FDR lower than the
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576 threshold will be highlighted in the plot.
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577
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578 -----
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579
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580 **Citations:**
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581
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582 .. class:: infomark
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583
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584 limma
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585
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586 Please cite the paper below for the limma software itself. Please also try
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587 to cite the appropriate methodology articles that describe the statistical
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588 methods implemented in limma, depending on which limma functions you are
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589 using. The methodology articles are listed in Section 2.1 of the limma
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590 User's Guide.
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591
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592 * Smyth, GK (2005). Limma: linear models for microarray data. In:
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593 'Bioinformatics and Computational Biology Solutions using R and
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594 Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
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595 W. Huber (eds), Springer, New York, pages 397-420.
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596
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597 .. class:: infomark
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598
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599 edgeR
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600
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601 Please cite the first paper for the software itself and the other papers for
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602 the various original statistical methods implemented in edgeR. See
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603 Section 1.2 in the User's Guide for more detail.
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604
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605 * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
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606 package for differential expression analysis of digital gene expression
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607 data. Bioinformatics 26, 139-140
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608
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609 * Robinson MD and Smyth GK (2007). Moderated statistical tests for assessing
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610 differences in tag abundance. Bioinformatics 23, 2881-2887
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611
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612 * Robinson MD and Smyth GK (2008). Small-sample estimation of negative
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613 binomial dispersion, with applications to SAGE data.
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614 Biostatistics, 9, 321-332
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615
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616 * McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis
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617 of multifactor RNA-Seq experiments with respect to biological variation.
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618 Nucleic Acids Research 40, 4288-4297
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619
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548802b3492f Version 1.0.9
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620 Report problems to: su.s@wehi.edu.au
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621
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622 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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623 .. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
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624 </help>
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625 </tool>