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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="R-module">riboSeqR</requirement>
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8 </requirements>
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9 <command interpreter="python">riboseqr/prepare.py
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10 #set $files_ribo = []
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11 #set $files_rna = []
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12 #set $replicates = []
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13
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14 #for $i, $s in enumerate($rnaseq.datasets)
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15 #silent $replicates.append($s.replicate_name.value)
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16 #silent $files_ribo.append($s.ribo_files.file_name)
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17 #try:
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18 #silent $s.rna_files
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19 #except:
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20 #pass
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21 #else:
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22 #silent $files_rna.append($s.rna_files.file_name)
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23 #end try
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24 #end for
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25
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26 #set $ribofiles = ", ".join($files_ribo)
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27 #set $rnafiles = ", ".join($files_rna)
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28 #set $replicate_names = ", ".join($replicates)
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29
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30 --ribo_files "$ribofiles"
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31 --rna_files "$rnafiles"
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32 --replicate_names "$replicate_names"
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33 --seqnames "$seqnames"
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34 --rdata_save "$rdata_save"
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35 --sam_format
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36 --html_file "$html_file"
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37 --output_path "$html_file.files_path"
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38 </command>
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39 <inputs>
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40 <conditional name="rnaseq">
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41 <param name="have-rnaseq" type="boolean" truevalue="checked"
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42 falsevalue="unchecked" label="Have RNA-Seq data?"/>
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43 <when value="checked">
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44 <repeat name="datasets" title="Ribo and RNA-Seq alignment"
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45 default="1">
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46 <param type="text" name="replicate_name" size="20"
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47 label="Provide a common name for each replicate group"
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48 value=""/>
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49 <param format="sam" name="ribo_files" type="data"
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50 label="Ribo-Seq alignment file (SAM)"
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51 multiple="false"/>
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52 <param format="sam" name="rna_files" type="data"
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53 label="RNA-Seq alignment file (SAM)"
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54 multiple="false"/>
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55 </repeat>
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56 </when>
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57 <when value="unchecked">
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58 <repeat name="datasets" title="Ribo-Seq alignment" default="1">
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59 <param type="text" name="replicate_name" size="20"
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60 label="Provide a common name for each replicate group"
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61 value=""/>
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62 <param format="sam" name="ribo_files" type="data"
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63 label="Ribo-Seq alignment file (SAM)"
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64 multiple="false">
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65 </param>
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66 </repeat>
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67 </when>
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68 </conditional>
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69 <param name="seqnames" type="text" area="True" label="Transcript (seqname)
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70 names to be read" size="3x60"
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71 help="[Optional] - only the mapped footprints for these transcripts will be
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72 used in further riboSeqR analysis. Multiple transcript names should
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73 be separated by commas. There should be no quotes around transcript names.">
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74 <sanitizer>
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75 <valid>
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76 <add value="|"/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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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="Prepare riboSeqR input (R data file)"/>
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84 <data format="html" name="html_file"
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85 label="Prepare riboSeqR input (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="ribo_files" value="12hRPF.sam" />
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90 <output name="html_file" file="Prepare_riboSeqR_input_(HTML_report).html">
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91 <extra_files type="file" name="RiboSeq file 1" value="RiboSeq file 1"/>
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92 </output>
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93 </test>
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94 </tests>
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95 <help>
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96 About
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97 -----
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98 This tool can be used to prepare input data for riboSeqR from SAM
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99 format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can
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100 do this alignment manually using bowtie or the
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101 "Transcriptome Mapping" -> "Align to transcriptome using Bowtie"
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102 tool on RiboGalaxy_
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103
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104 The required input format for riboSeqR_ is mentioned in the
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105 **"Getting Data"** section of the documentation_.
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106
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107 riboSeqR version: **1.0.4**.
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108
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109 How to use?
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110 -----------
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111 Inputs
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112 ......
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113 Select SAM format Ribo-Seq alignment files in the input section.
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114
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115 If you have RNA-Seq data, these can be included if the **"Have RNA-Seq data"**
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116 option is checked.
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117
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118 Outputs
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119 .......
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120 The following files will be generated on completion:
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121
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122 #. Prepare riboSeqR input (HTML report) - A HTML file with links to all other
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123 output files.
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124
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125 * Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
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126 These files are plain text and lines have the following information -
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127 strand, transcript name, alignment position, sequence.
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128
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129 Please note the alignments are made **0-indexed**.
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130
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131 * R script used in this session.
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132
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133 #. Prepare riboSeqR input (R data file) - used as input for the next step -
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134 *Triplet Periodicity*.
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135
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136 How are the SAM alignments processed?
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137 .....................................
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138 #. Lines starting with ``@`` are ignored.
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139 #. Lines having a ``FLAG=0`` are considered as successful alignments. These are
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140 considered for the next step.
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141 #. Alignment start is located on ``column 4``. These are decremented by
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142 1 as SAM alignments are 1-indexed.
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143 #. riboSeqR input file is written with the strand (``+``), transcript name,
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144 alignment start and the aligned sequence.
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145
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146 riboSeqR functions used
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147 .......................
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148 readRibodata.
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149
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150 For detailed description of the functions and the options used, please consult
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151 the riboSeqR documentation.
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152
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153 Links
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154 .....
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155 * `Bioconductor package information on riboSeqR`__
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156 * riboSeqR - `Reference manual`_
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157 * riboSeqR - `Introduction and workflow example`_
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158
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159 .. _RiboGalaxy: http://ribogalaxy.ucc.ie
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160
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161 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
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162
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163 __ riboSeqR_
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164
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165 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
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166
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167 .. _`Reference manual`: manual_
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168
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169 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
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170
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171 .. _`Introduction and workflow example`: documentation_
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172
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173 </help>
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174 </tool>
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