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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="R-module">riboSeqR</requirement>
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7 </requirements>
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8 <command interpreter="python">riboseqr/metagene.py
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9 --rdata_load "$rdata_load"
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10 --selected_lengths "$selected_lengths"
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11 --selected_frames "$selected_frames"
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12 --hit_mean "$hit_mean"
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13 --unique_hit_mean "$unique_hit_mean"
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14 --ratio_check "$ratio_check"
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15 --plot_lengths "$plot_lengths"
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16 --min5p "$min5p"
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17 --max5p "$max5p"
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18 --min3p "$min3p"
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19 --max3p "$max3p"
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20 --cap "$cap"
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21 --plot_title "$plot_title"
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22 --rdata_save "$rdata_save"
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23 --html_file "$html_file"
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24 --output_path "$html_file.files_path"
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25 </command>
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26 <inputs>
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27 <param name="rdata_load" type="data" format="rda"
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28 label="Select Triplet periodicity (R data file)"
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29 multiple="false" optional="false"
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30 help="<br><h4><font color="#666666">filterHits parameters (footprint reads to be used in the analysis)</font></h4>">
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31 <validator type="expression"
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32 message="Please check if the correct RDA file is selected">value.name == "Triplet periodicity (R data file)"</validator>
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33 </param>
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34
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35 <param name="selected_lengths" type="text" value="27"
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36 label="Length of ribosome footprint
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37 reads to be used in filtering (lengths)"
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38 help="ex: 27,28. Multiple values must be comma-separated.
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39 Please consult Periodicity-report.txt." optional="false">
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40 <validator type="empty_field" message="Field requires a value"/>
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41 </param>
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42
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43 <param name="selected_frames" type="text" value=""
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44 label="Frames of the ribosome footprint reads to be used in filtering
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45 (frames)"
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46 help="ex: 1,0. Should be of equal length to the lengths parameter above.
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47 Multiple values must be comma-separated.
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48 Please consult the periodicity report from previous step."
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49 optional="false">
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50 <validator type="empty_field" message="Field requires a value"/>
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51 </param>
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52
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53 <param name="hit_mean" size="4" type="integer" value="10"
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54 label="Mean number of hits within a replicate group that
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55 should be observed to pass filtering (hitMean)" optional="false">
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56 <validator type="empty_field" message="Field requires a value"/>
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57 </param>
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58
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59 <param name="unique_hit_mean" size="4" type="integer" value="1"
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60 label="Mean number of unique sequences within a replicate group
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61 that should be observed to pass filtering
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62 (unqhitMean)" optional="false">
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63 <validator type="empty_field" message="Field requires a value"/>
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64 </param>
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65
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66 <param name="ratio_check" type="boolean" checked="yes"
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67 label="Check the ratios of the expected phase to maximal phase
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68 within the putative coding sequence
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69 (ratioCheck)" falsevalue="FALSE"
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70 truevalue="TRUE"
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71 help="<br><h4><font color="#666666">plotCDS parameters</font></h4>"/>
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72
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73 <param name="plot_lengths" type="text"
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74 label="Length of footprints to be
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75 plotted (lengths)"
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76 help="Multiple values should be comma-separated.
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77 In that case, multiple plots will be produced" value="27"/>
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78
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79 <param name="min5p" label="The distance upstream of the translation
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80 start to be plotted (min5p)" value="-20" type="integer"/>
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81
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82 <param name="max5p" label="The distance downstream of the translation
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83 start to be plotted (max5p)" value="200" type="integer"/>
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84
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85 <param name="min3p" label="The distance upstream of the translation
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86 end to be plotted (min3p)" value="-200" type="integer"/>
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87
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88 <param name="max3p" label="The distance downtream of the translation
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89 end to be plotted (max3p)" value="20" type="integer"/>
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90
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91 <param name="cap"
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92 label="If given, caps the height of plotted values (cap)"
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93 value="" type="integer" optional="true"/>
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94
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95 <param name="plot_title"
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96 label="Title of the plot (main)" type="text" size="30"
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97 value=""/>
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98 </inputs>
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99 <outputs>
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100 <data format="rda" name="rdata_save"
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101 label="Metagene analysis (R data file)"/>
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102 <data format="html" name="html_file"
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103 label="Metagene analysis (HTML report)"/>
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="rdata_load" value="Triplet periodicity (R data file)" ftype="rda"/>
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108 <param name="selected_lengths" value="28" />
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109 <param name="selected_frames" value="0" />
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110 <param name="plot_lengths" value="28" />
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111 <output name="html_file" file="Metagene_analysis_(HTML_report).html">
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112 <extra_files type="file" name="Metagene-analysis-plot1.png" value="Metagene-analysis-plot1.png"/>
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113 <extra_files type="file" name="Metagene-analysis-plot1.pdf" value="Metagene-analysis-plot1.pdf"/>
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114 </output>
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115 </test>
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116 </tests>
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117 <help>
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118 About
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119 -----
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120 Metagene analysis using riboSeqR. The input is the R data file from the previous
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121 step - Triplet periodicity.
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122
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123 riboSeqR version: **1.0.4**.
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124
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125 How to use?
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126 -----------
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127 Inputs
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128 ......
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129 #. Select **Triplet periodicity (R data file)** from the previous step.
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130
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131 #. Specify length of ribosome footprint reads to be used in filtering
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132 (lengths). Only these reads **will** be used in the analysis.
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133
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134 #. Specify frames to consider. This information can be obtained
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135 from the **Triplet periodicity (HTML report)**.
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136
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137 .. class:: warningmark
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138
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139 Please note that the frames specified should correspond to the
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140 lengths of the reads.
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141
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142 #. Under **plotCDS parameters**, input length of footprints to be considered for
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143 generating the plot.
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144
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145 #. Review/change other options if necessary and execute program.
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146
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147 Outputs
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148 .......
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149 The following files will be generated on completion:
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150
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151 #. Metagene analysis (HTML report)
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152
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153 A HTML file with results and links to other output files - plots for
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154 specified lengths (PDF) and R script used for the session.
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155
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156 #. Metagene analysis (R data file)
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157
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158 Used as input for the next step - *Plot Rribosome Profile*.
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159
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160 riboSeqR functions used
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161 .......................
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162 filterHits.
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163
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164 For detailed description of the functions and the options used, please consult
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165 the riboSeqR documentation.
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166
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167 Links
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168 .....
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169 * `Bioconductor package information on riboSeqR`__
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170 * riboSeqR - `Reference manual`_
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171 * riboSeqR - `Introduction and workflow example`_
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172
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173 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
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174
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175 __ riboSeqR_
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176
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177 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
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178
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179 .. _`Reference manual`: manual_
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180
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181 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
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182
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183 .. _`Introduction and workflow example`: documentation_
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184
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185 </help>
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186 </tool>
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