annotate riboplot.xml @ 21:3429405e2ce1

Add toolshed URL link in tool dependencies
author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Mon, 31 Aug 2015 14:54:40 +0100
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1 <tool id="riboplot" name="riboplot" version="0.1.0">
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2 <description>Plot and output read counts for a single transcript in an alignment (BAM)
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3 </description>
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4 <requirements>
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5 <requirement type="package" version="0.1.0">riboplot</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error" />
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9 </stdio>
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10 <command interpreter="python">riboplot
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11 --ribo_file "${ribo_file}"
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12 --transcriptome_fasta "${transcriptome_fasta}"
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13 --transcript_name "${transcript_name}"
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14 #if $rnacov.rnacov_select=="yes"
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15 --rna_file "${rna_file}"
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16 #end if
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17 --read_length "${read_length}"
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18 --read_offset "${read_offset}"
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19 --html_file "${html_file}"
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20 --output_path "${html_file.files_path}"
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21 ## --debug
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22 </command>
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23 <inputs>
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24 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
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25 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
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26 <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
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27 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
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28 <validator type="empty_field" message="Field requires a value"/>
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29 <sanitizer>
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30 <valid>
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31 <add value="|"/>
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32 </valid>
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33 </sanitizer>
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34 </param>
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35 <conditional name="rnacov">
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36 <param name="rnacov_select" type="select" label="Include RNA Coverage">
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37 <option value="no">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <when value="yes">
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41 <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
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42 </when>
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43 <when value="no" />
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44 </conditional>
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45 <param name="read_length" type="integer" label="Read length to consider" value="28"/>
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46 <param name="read_offset" type="integer" label="Offset" value="0"/>
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47 </inputs>
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48 <outputs>
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49 <data format="html" name="html_file" label="riboplot (HTML report)"/>
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50 </outputs>
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51 <help>
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52 **RiboPlot**
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53
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54 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM).
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56 ----
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57
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58 **Parameters**
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60 1. Ribo-Seq alignment file (Sorted BAM file)
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61
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62 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
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63 file should be sorted. This can be done using one of the following methods.
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64
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65 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
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66 2. ``samtools sort input.bam inputsorted``
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67
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68 2. Transcriptome (FASTA)
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69
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70 A FASTA format file with sequences of the transcripts.
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71
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72 3. Name of the transcript to plot (Text)
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73
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74 The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
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75 and the Ribo-Seq/RNA-Seq alignment (BAM).
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76
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77 4. RNA coverage [optional] (Sorted BAM file)
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79 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
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80
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81 5. Read lengths to consider [Optional] (Integer - 0 or greater)
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83 If this option is provided, only Ribo-Seq data of the given length is considered.
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84
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85 6. Offset [optional] (Integer - 0 or greater)
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86
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87 If this option is provided, this offset is added to the read alignment positions.
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88
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89 ----
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90
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91 **Output**
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92
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93 1. Plots (PNG and SVG)
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94
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95 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
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96
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97 RNA coverage as a gray background (if the RNA coverage option was selected).
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98
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99 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.
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100
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101 The color codes are start (white) and stop (dark gray).
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102
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103 .. image:: images/riboplot.png
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104
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105 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)
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106
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107 </help>
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108 </tool>