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author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 27 Oct 2015 12:29:39 +0000
parents b2eb07000039
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1 <tool id="riboseqr_prepare_input" name="Prepare riboSeqR input" version="0.4.0">
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2 <description>
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3 (Step 1) Prepare alignment file (SAM format, Ribo-Seq or RNA-Seq alignments)
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4 for riboSeqR analysis.
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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/prepare.py
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16 #set $files_ribo = []
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17 #set $files_rna = []
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18 #set $replicates = []
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19
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20 #for $i, $s in enumerate($rnaseq.datasets)
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21 #silent $replicates.append($s.replicate_name.value)
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22 #silent $files_ribo.append($s.ribo_files.file_name)
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23 #try:
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24 #silent $s.rna_files
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25 #except:
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26 #pass
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27 #else:
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28 #silent $files_rna.append($s.rna_files.file_name)
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29 #end try
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30 #end for
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31
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32 #set $ribofiles = ", ".join($files_ribo)
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33 #set $rnafiles = ", ".join($files_rna)
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34 #set $replicate_names = ", ".join($replicates)
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35
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36 --ribo_files "$ribofiles"
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37 --rna_files "$rnafiles"
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38 --replicate_names "$replicate_names"
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39 --seqnames "$seqnames"
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40 --rdata_save "$rdata_save"
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41 --sam_format
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42 --html_file "$html_file"
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43 --output_path "$html_file.files_path"
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44 </command>
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45 <inputs>
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46 <conditional name="rnaseq">
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47 <param name="have-rnaseq" type="boolean" truevalue="checked"
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48 falsevalue="unchecked" label="Have RNA-Seq data?"/>
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49 <when value="checked">
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50 <repeat name="datasets" title="Ribo and RNA-Seq alignment"
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51 default="1">
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52 <param type="text" name="replicate_name" size="20"
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53 label="Provide a common name for each replicate group"
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54 value=""/>
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55 <param format="sam" name="ribo_files" type="data"
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56 label="Ribo-Seq alignment file (SAM)"
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57 multiple="false"/>
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58 <param format="sam" name="rna_files" type="data"
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59 label="RNA-Seq alignment file (SAM)"
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60 multiple="false"/>
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61 </repeat>
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62 </when>
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63 <when value="unchecked">
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64 <repeat name="datasets" title="Ribo-Seq alignment" default="1">
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65 <param type="text" name="replicate_name" size="20"
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66 label="Provide a common name for each replicate group"
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67 value=""/>
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68 <param format="sam" name="ribo_files" type="data"
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69 label="Ribo-Seq alignment file (SAM)"
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70 multiple="false">
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71 </param>
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72 </repeat>
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73 </when>
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74 </conditional>
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75 <param name="seqnames" type="text" area="True" label="Transcript (seqname)
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76 names to be read" size="3x60"
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77 help="[Optional] - only the mapped footprints for these transcripts will be
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78 used in further riboSeqR analysis. Multiple transcript names should
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79 be separated by commas. There should be no quotes around transcript names.">
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80 <sanitizer>
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81 <valid>
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82 <add value="|"/>
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83 </valid>
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84 </sanitizer>
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85 </param>
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86 </inputs>
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87 <outputs>
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88 <data format="RData" name="rdata_save"
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89 label="Prepare riboSeqR input (R data file)"/>
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90 <data format="html" name="html_file"
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91 label="Prepare riboSeqR input (HTML report)"/>
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92 </outputs>
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93 <!--<tests>-->
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94 <!--<test>-->
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95 <!--<param name="ribo_files" value="12hRPF.sam" />-->
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96 <!--<output name="html_file" file="Prepare_riboSeqR_input_(HTML_report).html">-->
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97 <!--<extra_files type="file" name="RiboSeq file 1" value="RiboSeq file 1"/>-->
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98 <!--</output>-->
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99 <!--</test>-->
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100 <!--</tests>-->
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101 <help>
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102 Prepare riboSeqR Input
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103 ----------------------
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104 riboSeqR version: ``1.0.5``.
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105
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106 This tool can be used to prepare input data for riboSeqR from SAM
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107 format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can
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108 do this alignment manually using bowtie or using the
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109 "Transcriptome Mapping" -> "Align to transcriptome using Bowtie"
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110 tool on `RiboGalaxy &lt;http://ribogalaxy.ucc.ie&gt;`_.
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111
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112 The required input format for riboSeqR is mentioned in the
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113 "Getting Data" section of the documentation.
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114
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115 How to use?
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116 -----------
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117 Inputs
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118 ......
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119 Select SAM format Ribo-Seq alignment files in the input section.
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120
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121 If you have RNA-Seq data, these can be included if the *"Have RNA-Seq data"*
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122 option is checked.
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123
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124 Outputs
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125 .......
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126 The following files will be generated on completion:
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127
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128 #. Prepare riboSeqR input (HTML report) - A HTML file with links to all other
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129 output files.
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130
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131 #. Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
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132 These files are plain text and lines have the following information -
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133 strand, transcript name, alignment position, sequence.
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134
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135 .. class:: infomark
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136
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137 Please note the alignments are made **0-indexed**. Additional information on
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138 how the SAM alignments are processed can be found below.
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139
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140 #. R script used in this session.
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141
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142 #. Prepare riboSeqR input (R data file) - used as input for the next step -
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143 *Triplet Periodicity*.
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144
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145 How are the SAM alignments processed?
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146 .....................................
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147 #. Lines starting with ``@`` are ignored.
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148
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149 #. Lines having a ``FLAG=0`` are considered as successful alignments. These are
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150 considered for the next step.
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151
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152 #. Alignment start is located on ``column 4``. These are decremented by
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153 1 as SAM alignments are 1-indexed.
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154
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155 #. riboSeqR input file is written with the strand (``+``), transcript name,
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156 alignment start and the aligned sequence.
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157
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158 riboSeqR functions used
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159 .......................
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160 ``readRibodata``.
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161
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162 For detailed description of the functions and the options used, please consult
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163 the riboSeqR documentation.
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164
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165 Links
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166 .....
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167 `riboSeqR &lt;http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html&gt;`_
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168
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169 </help>
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170 <citations>
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171 <citation type="bibtex">
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172 @Manual{,
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173 title = {riboSeqR: Analysis of sequencing data from ribosome
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174 profiling experiments.},
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175 author = {Thomas J. Hardcastle},
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176 year = {2014},
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177 note = {R package version 1.0.5},
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178 }
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179 </citation>
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180 </citations>
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181 </tool>