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1 <tool id="riboseqr_ribosome_profile" name="Plot Ribosome Profile"
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2 version="0.4.0">
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3 <description>
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4 (Step 4) Plot Ribosome profile using riboSeqR.
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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/ribosome_profile.py
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10 --rdata_load "$rdata_load"
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11 --transcript_name "$transcript_name"
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12 --transcript_length "$transcript_length"
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13 --transcript_cap "$transcript_cap"
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14 --html_file "$html_file"
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15 --output_path "$html_file.files_path"
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16 </command>
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17 <inputs>
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18 <param name="rdata_load" format="rda" type="data"
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19 label="Select Metagene analysis (R data file)"
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20 multiple="false">
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21 <validator type="expression"
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22 message="Please check if the correct RDA file is selected">value.name == "Metagene analysis (R data file)"</validator>
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23 </param>
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24
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25 <param name="transcript_name" type="text" size="30"
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26 label="Name of the transcript to be plotted"
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27 help="Plot of ribosome footprint abundance and mRNA coverage
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28 (if available) for a specific transcript.">
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29 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
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30 <validator type="empty_field" message="Field requires a value"/>
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31 <sanitizer>
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32 <valid>
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33 <add value="|"/>
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34 </valid>
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35 </sanitizer>
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36 </param>
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37
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38 <param name="transcript_length" type="text"
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39 label="Select Ribosome footprint length"
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40 help="" value="28">
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41 <validator type="expression" message="Please input a single footprint length">len(value.split(',')) == 1</validator>
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42 <validator type="expression" message="Please input a single footprint length">len(value.split(' ')) == 1</validator>
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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="transcript_cap" type="integer" value="200"
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47 label="Cap on the largest value that will be plotted as an
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48 abundance of the ribosome footprint data"/>
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49 </inputs>
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50 <outputs>
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51 <data format="html" name="html_file"
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52 label="Plot ribosome profile (HTML report)"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="rdata_load" value="Metagene analysis (R data file)" />
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57 <param name="transcript_name" value="gi|31340752|ref|NM_178437.2|" />
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58 <param name="transcript_length" value="28" />
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59 <param name="transcript_cap" value="200" />
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60 <output name="html_file" file="Plot_ribosome_profile_(HTML_report).html">
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61 <extra_files type="file" name="Ribosome-profile-plot.png" value="Ribosome-profile-plot.png" ftype="png" />
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62 <extra_files type="file" name="Ribosome-profile-plot.pdf" value="Ribosome-profile-plot.pdf" ftype="pdf" />
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63 </output>
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64 </test>
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65 </tests>
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66 <requirements>
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67 <requirement type="R-module">riboSeqR</requirement>
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68 </requirements>
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69 <help>
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70 About
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71 -----
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72 This tool can be used for generating a ribosome profile plot for a given
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73 transcript. The input is the R data file from the previous
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74 step - Metagene analysis.
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75
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76 riboSeqR version: **1.0.4**.
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77
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78 How to use?
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79 -----------
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80 Inputs
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81 ......
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82 Select **Metagene analysis (R data file)** from the previous step, enter name
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83 of the transcript to plot, review/change parameters and execute program.
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84
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85 .. class:: warningmark
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86
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87 The transcript name should correspond to names used in SAM alignments
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88 and FASTA file of the transcriptome.
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89
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90 Outputs
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91 .......
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92 The following files will be generated on completion:
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93
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94 Plot ribosome profile (HTML report)
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95
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96 A HTML file with results and links to other output files - plot for the
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97 specified transcript (PDF) and R script used for the session.
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98
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99 riboSeqR functions used
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100 .......................
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101 plotTranscript.
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102
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103 For detailed description of the functions and the options used, please consult
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104 the riboSeqR documentation.
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105
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106 Links
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107 .....
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108 * `Bioconductor package information on riboSeqR`__
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109 * riboSeqR - `Reference manual`_
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110 * riboSeqR - `Introduction and workflow example`_
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111
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112 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
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113
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114 __ riboSeqR_
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115
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116 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
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117
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118 .. _`Reference manual`: manual_
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119
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120 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
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121
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122 .. _`Introduction and workflow example`: documentation_
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123
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124 </help>
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125 </tool>
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