Mercurial > repos > vimalkumarvelayudhan > riboplot
annotate riboplot.xml @ 19:6e3b13906b54
Use packages from the test toolshed. Add bedtools dependency
author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
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date | Fri, 28 Aug 2015 11:07:26 +0100 |
parents | 844eb8c36f32 |
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3 | 1 <tool id="riboplot" name="riboplot" version="0.1.0"> |
2 <description>Plot and output read counts for a single transcript in an alignment (BAM) | |
3 </description> | |
4 <requirements> | |
5 <requirement type="package" version="1.2.1">matplotlib</requirement> | |
6 <requirement type="package" version="0.8.3">pysam</requirement> | |
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7 <requirement type="package" version="2.18">bedtools</requirement> |
3 | 8 </requirements> |
9 <stdio> | |
10 <exit_code range="1:" level="fatal" description="Error" /> | |
11 </stdio> | |
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12 <command interpreter="python">riboplot/riboplot.py |
3 | 13 --ribo_file "${ribo_file}" |
14 --transcriptome_fasta "${transcriptome_fasta}" | |
15 --transcript_name "${transcript_name}" | |
16 #if $rnacov.rnacov_select=="yes" | |
17 --rna_file "${rna_file}" | |
18 #end if | |
19 --read_length "${read_length}" | |
20 --read_offset "${read_offset}" | |
21 --html_file "${html_file}" | |
22 --output_path "${html_file.files_path}" | |
23 ## --debug | |
24 </command> | |
25 <inputs> | |
26 <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> | |
27 <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> | |
28 <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40"> | |
29 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator> | |
30 <validator type="empty_field" message="Field requires a value"/> | |
31 <sanitizer> | |
32 <valid> | |
33 <add value="|"/> | |
34 </valid> | |
35 </sanitizer> | |
36 </param> | |
37 <conditional name="rnacov"> | |
38 <param name="rnacov_select" type="select" label="Include RNA Coverage"> | |
39 <option value="no">No</option> | |
40 <option value="yes">Yes</option> | |
41 </param> | |
42 <when value="yes"> | |
43 <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/> | |
44 </when> | |
45 <when value="no" /> | |
46 </conditional> | |
47 <param name="read_length" type="integer" label="Read length to consider" value="28"/> | |
48 <param name="read_offset" type="integer" label="Offset" value="0"/> | |
49 </inputs> | |
50 <outputs> | |
51 <data format="html" name="html_file" label="riboplot (HTML report)"/> | |
52 </outputs> | |
53 <help> | |
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54 **RiboPlot** |
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55 |
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56 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). |
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57 |
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58 ---- |
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59 |
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60 **Parameters** |
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61 |
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62 1. Ribo-Seq alignment file (Sorted BAM file) |
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63 |
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64 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM |
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65 file should be sorted. This can be done using one of the following methods. |
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66 |
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67 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. |
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68 2. ``samtools sort input.bam inputsorted`` |
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69 |
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70 2. Transcriptome (FASTA) |
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71 |
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72 A FASTA format file with sequences of the transcripts. |
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73 |
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74 3. Name of the transcript to plot (Text) |
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75 |
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76 The name of the transcript to plot **should** match the name in the transcriptome (FASTA) |
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77 and the Ribo-Seq/RNA-Seq alignment (BAM). |
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78 |
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79 4. RNA coverage [optional] (Sorted BAM file) |
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80 |
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81 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. |
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82 |
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83 5. Read lengths to consider [Optional] (Integer - 0 or greater) |
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84 |
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85 If this option is provided, only Ribo-Seq data of the given length is considered. |
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86 |
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87 6. Offset [optional] (Integer - 0 or greater) |
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88 |
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89 If this option is provided, this offset is added to the read alignment positions. |
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90 |
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91 ---- |
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92 |
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93 **Output** |
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94 |
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95 1. Plots (PNG and SVG) |
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96 |
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97 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) |
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98 |
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99 RNA coverage as a gray background (if the RNA coverage option was selected). |
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100 |
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101 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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102 |
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103 The color codes are start (white) and stop (dark gray). |
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104 |
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105 .. image:: images/riboplot.png |
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106 |
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107 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) |
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108 |
3 | 109 </help> |
110 </tool> |