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author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents d7ce95ccf54f
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1 <tool id="riboseqr_metagene" name="Metagene Analysis" version="0.4.0">
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2 <description>
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3 (Step 3) Metagene analysis using riboSeqR.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="package" version="6.2">readline</requirement>
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8 <requirement type="package" version="2.3.10">rpy2</requirement>
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9 <requirement type="package" version="0.4.0">riboseqr_wrapper_deps</requirement>
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10 </requirements>
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11 <command interpreter="python">riboseqr/metagene.py
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12 --rdata_load "$rdata_load"
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13 --selected_lengths "$selected_lengths"
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14 --selected_frames "$selected_frames"
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15 --hit_mean "$hit_mean"
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16 --unique_hit_mean "$unique_hit_mean"
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17 --ratio_check "$ratio_check"
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18 --plot_lengths "$plot_lengths"
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19 --min5p "$min5p"
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20 --max5p "$max5p"
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21 --min3p "$min3p"
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22 --max3p "$max3p"
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23 --cap "$cap"
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24 --plot_title "$plot_title"
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25 --rdata_save "$rdata_save"
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26 --html_file "$html_file"
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27 --output_path "$html_file.files_path"
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28 </command>
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29 <inputs>
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30 <param name="rdata_load" type="data" format="RData"
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31 label="Select Triplet periodicity (R data file)"
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32 multiple="false" optional="false"
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33 help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;filterHits parameters (footprint reads to be used in the analysis)&lt;/font&gt;&lt;/h4&gt;">
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34 <validator type="expression"
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35 message="Please check if the correct RDA file is selected">value.name == "Triplet periodicity (R data file)"</validator>
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36 </param>
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37
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38 <param name="selected_lengths" type="text" value="27"
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39 label="Length of ribosome footprint
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40 reads to be used in filtering (lengths)"
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41 help="ex: 27,28. Multiple values must be comma-separated.
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42 Please consult Periodicity-report.txt." optional="false">
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43 <validator type="empty_field" message="Field requires a value"/>
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44 </param>
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45
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46 <param name="selected_frames" type="text" value=""
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47 label="Frames of the ribosome footprint reads to be used in filtering
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48 (frames)"
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49 help="ex: 1,0. Should be of equal length to the lengths parameter above.
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50 Multiple values must be comma-separated.
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51 Please consult the periodicity report from previous step."
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52 optional="false">
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53 <validator type="empty_field" message="Field requires a value"/>
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54 </param>
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55
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56 <param name="hit_mean" size="4" type="integer" value="10"
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57 label="Mean number of hits within a replicate group that
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58 should be observed to pass filtering (hitMean)" optional="false">
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59 <validator type="empty_field" message="Field requires a value"/>
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60 </param>
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61
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62 <param name="unique_hit_mean" size="4" type="integer" value="1"
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63 label="Mean number of unique sequences within a replicate group
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64 that should be observed to pass filtering
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65 (unqhitMean)" optional="false">
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66 <validator type="empty_field" message="Field requires a value"/>
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67 </param>
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68
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69 <param name="ratio_check" type="boolean" checked="yes"
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70 label="Check the ratios of the expected phase to maximal phase
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71 within the putative coding sequence
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72 (ratioCheck)" falsevalue="FALSE"
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73 truevalue="TRUE"
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74 help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotCDS parameters&lt;/font&gt;&lt;/h4&gt;"/>
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75
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76 <param name="plot_lengths" type="text"
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77 label="Length of footprints to be
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78 plotted (lengths)"
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79 help="Multiple values should be comma-separated.
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80 In that case, multiple plots will be produced" value="27"/>
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81
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82 <param name="min5p" label="The distance upstream of the translation
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83 start to be plotted (min5p)" value="-20" type="integer"/>
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84
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85 <param name="max5p" label="The distance downstream of the translation
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86 start to be plotted (max5p)" value="200" type="integer"/>
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87
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88 <param name="min3p" label="The distance upstream of the translation
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89 end to be plotted (min3p)" value="-200" type="integer"/>
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90
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91 <param name="max3p" label="The distance downtream of the translation
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92 end to be plotted (max3p)" value="20" type="integer"/>
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93
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94 <param name="cap"
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95 label="If given, caps the height of plotted values (cap)"
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96 value="" type="integer" optional="true"/>
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97
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98 <param name="plot_title"
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99 label="Title of the plot (main)" type="text" size="30"
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100 value=""/>
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101 </inputs>
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102 <stdio>
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103 <exit_code range="1:" level="fatal" description="Error" />
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104 </stdio>
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105 <outputs>
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106 <data format="RData" name="rdata_save"
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107 label="Metagene analysis (R data file)"/>
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108 <data format="html" name="html_file"
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109 label="Metagene analysis (HTML report)"/>
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110 </outputs>
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111 <!--<tests>-->
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112 <!--<test>-->
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113 <!--<param name="rdata_load" value="Triplet periodicity (R data file)" ftype="RData"/>-->
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114 <!--<param name="hit_mean" value="50"/>-->
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115 <!--<param name="unique_hit_mean" value="10"/>-->
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116 <!--<param name="min5p" value="-20"/>-->
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117 <!--<param name="max5p" value="200"/>-->
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118 <!--<param name="min3p" value="-200"/>-->
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119 <!--<param name="max3p" value="20"/>-->
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120 <!--<param name="cap" value=""/>-->
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121 <!--<param name="plot_title" value=""/>-->
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122 <!--<output name="rdata_save" file="Metagene analysis (R data file)" ftype="RData"/>-->
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123 <!--<output name="html_file" file="Metagene_analysis_(HTML_report).html">-->
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124 <!--<extra_files type="file" name="Metagene-analysis-plot1.pdf" value="Metagene-analysis-plot1.pdf"/>-->
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125 <!--<extra_files type="file" name="Metagene-analysis-plot1_1.png" value="Metagene-analysis-plot1_1.png"/>-->
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126 <!--<extra_files type="file" name="Metagene-analysis-plot1_2.png" value="Metagene-analysis-plot1_2.png"/>-->
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127 <!--<extra_files type="file" name="Metagene-analysis-plot1_3.png" value="Metagene-analysis-plot1_3.png"/>-->
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128 <!--<extra_files type="file" name="Metagene-analysis-plot1_4.png" value="Metagene-analysis-plot1_4.png"/>-->
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129 <!--<extra_files type="file" name="Metagene-analysis-plot2.pdf" value="Metagene-analysis-plot2.pdf"/>-->
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130 <!--<extra_files type="file" name="Metagene-analysis-plot2_1.png" value="Metagene-analysis-plot2_1.png"/>-->
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131 <!--<extra_files type="file" name="Metagene-analysis-plot2_2.png" value="Metagene-analysis-plot2_2.png"/>-->
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132 <!--<extra_files type="file" name="Metagene-analysis-plot2_3.png" value="Metagene-analysis-plot2_3.png"/>-->
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133 <!--<extra_files type="file" name="Metagene-analysis-plot2_4.png" value="Metagene-analysis-plot2_4.png"/>-->
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134 <!--</output>-->
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135 <!--</test>-->
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136 <!--</tests>-->
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137 <help>
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138 Metagene Analysis
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139 -----------------
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140 riboSeqR version: ``1.0.5``.
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141
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142 The input is the R data file from the previous step - Triplet periodicity.
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143
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144 How to use?
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145 -----------
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146 Inputs
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147 ......
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148 #. Select *Triplet periodicity (R data file)* from the previous step.
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149
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150 #. Specify length of ribosome footprint reads to be used in filtering
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151 (lengths). Only these reads **will** be used in the analysis.
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152
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153 #. Specify frames to consider. This information can be obtained
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154 from the *Triplet periodicity (HTML report)*.
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155
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156 .. class:: warningmark
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157
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158 Please note that the frames specified should correspond to the
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159 lengths of the reads.
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160
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161 #. Under *plotCDS parameters*, input length of footprints to be considered for
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162 generating the plot.
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163
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164 #. Review/change other options if necessary and execute program.
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165
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166 Outputs
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167 .......
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168 The following files will be generated on completion:
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169
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170 #. Metagene analysis (HTML report)
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171
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172 A HTML file with results and links to other output files - plots for
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173 specified lengths (PDF) and R script used for the session.
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174
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175 #. Metagene analysis (R data file)
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176
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177 Used as input for the next step - *Plot Rribosome Profile*.
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178
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179 riboSeqR functions used
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180 .......................
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181 ``filterHits``.
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182
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183 For detailed description of the functions and the options used, please consult
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184 the riboSeqR documentation.
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185
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186 Links
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187 .....
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188 `riboSeqR &lt;http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html&gt;`_.
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189
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190 </help>
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191 <citations>
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192 <citation type="bibtex">
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193 @Manual{,
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194 title = {riboSeqR: Analysis of sequencing data from ribosome
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195 profiling experiments.},
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196 author = {Thomas J. Hardcastle},
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197 year = {2014},
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198 note = {R package version 1.0.5},
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199 }
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200 </citation>
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201 </citations>
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202 </tool>