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1 <tool id="riboseqr_triplet_periodicity" name="Triplet Periodicity"
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2 version="0.4.0">
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3 <description>
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4 (Step 2) Plot triplet periodicity for different read lengths.
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5 </description>
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6 <requirements>
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7 <requirement type="R-module">riboSeqR</requirement>
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8 </requirements>
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9 <command interpreter="python">riboseqr/triplet.py
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10 --rdata_load "$rdata_load"
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11 --fasta_file "$fasta_file"
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12 --start_codons "$start_codons"
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13 --stop_codons "$stop_codons"
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14 --include_lengths "$include_lengths"
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15 --analyze_plot_lengths "$analyze_plot_lengths"
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16 --text_legend "$text_legend"
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17 --rdata_save "$rdata_save"
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18 --html_file "$html_file"
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19 --output_path "$html_file.files_path"
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20 </command>
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21 <inputs>
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22 <param name="rdata_load" type="data" format="rda"
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23 label="Select prepared riboSeqR input (R data file)"
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24 multiple="false" optional="false"
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25 help="<br><h4><font color="#666666">findCDS
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26 parameters</font></h4>">
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27 <validator type="expression"
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28 message="Please check if the correct RDA file is selected">value.name == "Prepare riboSeqR input (R data file)"</validator>
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29 </param>
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30
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31 <param format="fasta" name="fasta_file" type="data"
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32 label="Select FASTA file of the reference transcriptome"
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33 help="This Fasta file is used to find start (ATG) and
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34 stop codons(TAG, TAA, TGA) in frame with one another. If no files
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35 are listed, you will need to upload a FASTA file of the reference
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36 transcriptome.">
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37 <validator type="empty_field" message="Field requires a value"/>
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38 </param>
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39
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40 <param name="start_codons" type="text" size="15" value="ATG"
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41 label="Start codon(s) to use"
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42 help="Default is ATG. Multiple values must be comma-separated.">
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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="stop_codons" type="text" size="15" value="TAG, TAA, TGA"
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47 label="Stop codon(s) to use"
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48 help="Default is TAG, TAA, TGA. Multiple values must be comma-separated.
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49 <h4><font color="#666666">frameCounting
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50 parameters</font></h4>">
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51 <validator type="empty_field" message="Field requires a value"/>
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52 </param>
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53
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54 <param name="include_lengths" type="text"
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55 label="Lengths of ribosome footprints
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56 to be included"
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57 help="Here, you can specify the lengths of ribosome footprints to
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58 be included in the riboData object. <br>For example 25:30.
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59 Range, semi-colon separated. <h4><font color="#666666">readingFrame
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60 parameters</font></h4>" value="25:30"/>
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61
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62 <param name="analyze_plot_lengths" type="text"
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63 label="Lengths of reads to be analysed for frame-shift, or to be plotted"
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64 help="[Optional] If omitted, all lengths will be plotted.
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65 <br>For example 26:30. Range, semi-colon separated.
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66 <h4><font color="#666666">plotFS
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67 parameters</font></h4>" value="26:30"/>
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68
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69 <param name="text_legend" type="text" size="30"
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70 value='Frame 0, Frame 1, Frame 2'
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71 label="Text for legend used in the
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72 plot" help="Comma-separated values."/>
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73 </inputs>
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74 <outputs>
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75 <data format="rda" name="rdata_save"
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76 label="Triplet periodicity (R data file)"/>
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77 <data format="html" name="html_file"
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78 label="Triplet periodicity (HTML report)"/>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda"/>
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83 <param name="fasta_file" value="zebrafish.fasta.bz2" />
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84 <param name="include_lengths" value="25:30" />
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85 <param name="analyze_plot_lengths" value="26:30" />
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86 <output name="html_file" file="Triplet_periodicity_(HTML_report).html">
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87 <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png"/>
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88 <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf"/>
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89 </output>
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90 </test>
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91 </tests>
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92 <help>
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93 About
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94 -----
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95 This tool can be used to plot triplet periodicity for different read lengths.
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96 The inputs for this program are
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97
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98 #. Prepare riboSeqR input (R data file) from the previous step.
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99 #. FASTA format file of the reference transcriptome.
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100
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101 riboSeqR version: **1.0.4**.
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102
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103 How to use?
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104 -----------
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105 Inputs
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106 ......
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107 Select prepared R data file from the previous step.
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108
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109 Select FASTA format file of the reference transcriptome, review/change other
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110 options if necessary and execute program.
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111
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112 Outputs
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113 .......
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114 The following files will be generated on completion:
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115
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116 #. Triplet periodicity (HTML report)
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117
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118 A HTML file with results and links to other output files - triplet
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119 periodicity plot (PDF) and R script used for the session.
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120
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121 #. Triplet periodicity (R data file)
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122
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123 Used as input for the next step - *Metagene analysis*.
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124
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125 riboSeqR functions used
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126 .......................
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127 findCDS, frameCounting, readingFrame and plotFS.
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128
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129 For detailed description of the functions and the options used, please consult
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130 the riboSeqR documentation.
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131
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132 Links
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133 .....
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134 * `Bioconductor package information on riboSeqR`__
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135 * riboSeqR - `Reference manual`_
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136 * riboSeqR - `Introduction and workflow example`_
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137
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138 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
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139
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140 __ riboSeqR_
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141
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142 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
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143
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144 .. _`Reference manual`: manual_
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145
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146 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
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147
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148 .. _`Introduction and workflow example`: documentation_
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149
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150 </help>
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151 </tool>
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