annotate riboplot.xml @ 17:805b779d4013

Fix tool dependencies
author Vimalkumar Velayudhan <vimal@biotechcoder.com>
date Mon, 31 Aug 2015 11:41:48 +0100
parents 844eb8c36f32
children cff63cf0dea8 6e3b13906b54
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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="1.2.1">matplotlib</requirement>
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6 <requirement type="package" version="0.8.3">pysam</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error" />
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10 </stdio>
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11 <command interpreter="python">riboplot/riboplot.py
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12 --ribo_file "${ribo_file}"
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13 --transcriptome_fasta "${transcriptome_fasta}"
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14 --transcript_name "${transcript_name}"
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15 #if $rnacov.rnacov_select=="yes"
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16 --rna_file "${rna_file}"
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17 #end if
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18 --read_length "${read_length}"
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19 --read_offset "${read_offset}"
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20 --html_file "${html_file}"
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21 --output_path "${html_file.files_path}"
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22 ## --debug
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23 </command>
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24 <inputs>
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25 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
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26 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
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27 <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
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28 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
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29 <validator type="empty_field" message="Field requires a value"/>
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30 <sanitizer>
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31 <valid>
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32 <add value="|"/>
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33 </valid>
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34 </sanitizer>
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35 </param>
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36 <conditional name="rnacov">
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37 <param name="rnacov_select" type="select" label="Include RNA Coverage">
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38 <option value="no">No</option>
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39 <option value="yes">Yes</option>
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40 </param>
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41 <when value="yes">
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42 <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
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43 </when>
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44 <when value="no" />
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45 </conditional>
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46 <param name="read_length" type="integer" label="Read length to consider" value="28"/>
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47 <param name="read_offset" type="integer" label="Offset" value="0"/>
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="html_file" label="riboplot (HTML report)"/>
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51 </outputs>
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52 <help>
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53 **RiboPlot**
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54
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55 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
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59 **Parameters**
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60
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61 1. Ribo-Seq alignment file (Sorted BAM file)
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62
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63 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
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64 file should be sorted. This can be done using one of the following methods.
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65
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66 1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
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67 2. ``samtools sort input.bam inputsorted``
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68
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69 2. Transcriptome (FASTA)
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70
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71 A FASTA format file with sequences of the transcripts.
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72
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73 3. Name of the transcript to plot (Text)
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74
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75 The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
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76 and the Ribo-Seq/RNA-Seq alignment (BAM).
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77
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78 4. RNA coverage [optional] (Sorted BAM file)
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79
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80 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
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81
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82 5. Read lengths to consider [Optional] (Integer - 0 or greater)
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83
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84 If this option is provided, only Ribo-Seq data of the given length is considered.
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85
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86 6. Offset [optional] (Integer - 0 or greater)
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87
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88 If this option is provided, this offset is added to the read alignment positions.
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89
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90 ----
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91
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92 **Output**
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93
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94 1. Plots (PNG and SVG)
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95
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96 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)
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97
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98 RNA coverage as a gray background (if the RNA coverage option was selected).
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99
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100 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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101
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102 The color codes are start (white) and stop (dark gray).
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103
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104 .. image:: images/riboplot.png
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105
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106 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)
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107
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108 </help>
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109 </tool>