Mercurial > repos > vimalkumarvelayudhan > riboseqr_wrapper

annotate triplet.xml @ 0:c34c364ce75d

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author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Tue, 21 Jul 2015 14:48:39 +0100
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children b2eb07000039
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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="package" version="3.1.2">R</requirement>
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8 <requirement type="package" version="6.2">readline</requirement>
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9 <requirement type="package" version="2.3.10">rpy2</requirement>
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10 <requirement type="package" version="0.4.0">riboseqr_wrapper_deps</requirement>
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11 </requirements>
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12 <stdio>
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13 <exit_code range="1:" level="fatal" description="Error" />
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14 </stdio>
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15 <command interpreter="python">riboseqr/triplet.py
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16 --rdata_load "$rdata_load"
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17 --fasta_file "$fasta_file"
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18 --start_codons "$start_codons"
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19 --stop_codons "$stop_codons"
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20 --include_lengths "$include_lengths"
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21 --analyze_plot_lengths "$analyze_plot_lengths"
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22 --text_legend "$text_legend"
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23 --rdata_save "$rdata_save"
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24 --html_file "$html_file"
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25 --output_path "$html_file.files_path"
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26 </command>
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27 <inputs>
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28 <param name="rdata_load" type="data" format="rda"
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29 label="Select prepared riboSeqR input (R data file)"
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30 multiple="false" optional="false"
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31 help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;findCDS
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32 parameters&lt;/font&gt;&lt;/h4&gt;">
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33 <validator type="expression"
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34 message="Please check if the correct RDA file is selected">value.name == "Prepare riboSeqR input (R data file)"</validator>
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35 </param>
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36
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37 <param format="fasta" name="fasta_file" type="data"
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38 label="Select FASTA file of the reference transcriptome"
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39 help="This Fasta file is used to find start (ATG) and
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40 stop codons(TAG, TAA, TGA) in frame with one another. If no files
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41 are listed, you will need to upload a FASTA file of the reference
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42 transcriptome. Please note that the FASTA header of the transcriptome
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43 sequences must match the sequence names from the SAM file.">
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44 <validator type="empty_field" message="Field requires a value"/>
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45 </param>
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46
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47 <param name="start_codons" type="text" size="15" value="ATG"
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48 label="Start codon(s) to use"
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49 help="Default is ATG. Multiple values must be comma-separated.">
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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="stop_codons" type="text" size="15" value="TAG, TAA, TGA"
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54 label="Stop codon(s) to use"
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55 help="Default is TAG, TAA, TGA. Multiple values must be comma-separated.
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56 &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;frameCounting
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57 parameters&lt;/font&gt;&lt;/h4&gt;">
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58 <validator type="empty_field" message="Field requires a value"/>
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59 </param>
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60
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61 <param name="include_lengths" type="text"
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62 label="Lengths of ribosome footprints
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63 to be included"
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64 help="Here, you can specify the lengths of ribosome footprints to
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65 be included in the riboData object. &lt;br&gt;For example 25:30.
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66 Range, semi-colon separated. &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;readingFrame
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67 parameters&lt;/font&gt;&lt;/h4&gt;" value="25:30"/>
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68
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69 <param name="analyze_plot_lengths" type="text"
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70 label="Lengths of reads to be analysed for frame-shift, or to be plotted"
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71 help="[Optional] If omitted, all lengths will be plotted.
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72 &lt;br&gt;For example 26:30. Range, semi-colon separated.
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73 &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotFS
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74 parameters&lt;/font&gt;&lt;/h4&gt;" value="26:30"/>
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75
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76 <param name="text_legend" type="text" size="30"
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77 value='Frame 0, Frame 1, Frame 2'
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78 label="Text for legend used in the
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79 plot" help="Comma-separated values."/>
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80 </inputs>
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81 <outputs>
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82 <data format="rda" name="rdata_save"
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83 label="Triplet periodicity (R data file)"/>
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84 <data format="html" name="html_file"
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85 label="Triplet periodicity (HTML report)"/>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda" />
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90 <param name="fasta_file" value="rsem_chlamy236_deNovo.transcripts.fa" />
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91 <param name="include_lengths" value="25:30" />
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92 <param name="analyze_plot_lengths" value="26:30" />
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93 <output name="rdata_save" file="Triplet periodicity (R data file)" ftype="rda" />
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94 <output name="html_file" file="Triplet_periodicity_(HTML_report).html">
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95 <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png" />
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96 <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf" />
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97 </output>
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98 </test>
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99 </tests>
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100 <help>
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101 Triplet Periodicity
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102 -------------------
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103 riboSeqR version: ``1.0.5``.
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104
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105 This tool can be used to plot triplet periodicity for different read lengths.
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106 The inputs for this program are:
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107
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108 #. Prepare riboSeqR input (R data file) from the previous step.
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109 #. FASTA format file of the reference transcriptome.
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110
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111 .. class:: infomark
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112
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113 Please note that the FASTA header of the transcriptome sequences must
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114 match the sequence names from the SAM file.
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115
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116 How to use?
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117 -----------
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118 Inputs
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119 ......
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120 Select prepared R data file from the previous step.
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121
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122 Select FASTA format file of the reference transcriptome, review/change other
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123 options if necessary and execute program.
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124
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125 Outputs
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126 .......
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127 The following files will be generated on completion:
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128
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129 #. Triplet periodicity (HTML report)
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130
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131 A HTML file with results and links to other output files - triplet
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132 periodicity plot (PDF) and R script used for the session.
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133
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134 #. Triplet periodicity (R data file)
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135
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136 Used as input for the next step - *Metagene analysis*.
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137
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138 riboSeqR functions used
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139 .......................
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140 ``findCDS``, ``frameCounting``, ``readingFrame`` and ``plotFS``.
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141
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142 For detailed description of the functions and the options used, please consult
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143 the riboSeqR documentation.
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144
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145 Links
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146 .....
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147 `riboSeqR &lt;http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html&gt;`_.
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148
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149 </help>
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150 <citations>
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151 <citation type="bibtex">
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152 @Manual{,
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153 title = {riboSeqR: Analysis of sequencing data from ribosome
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154 profiling experiments.},
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155 author = {Thomas J. Hardcastle},
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156 year = {2014},
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157 note = {R package version 1.0.5},
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158 }
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159 </citation>
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160 </citations>
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161 </tool>