Mercurial > repos > vimalkumarvelayudhan > riboplot
comparison riboplot.xml @ 8:844eb8c36f32
Add help section in xml and update usage documentation
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
---|---|
date | Mon, 17 Aug 2015 10:27:58 +0100 |
parents | 1901dcdc12ff |
children | cff63cf0dea8 6e3b13906b54 |
comparison
equal
deleted
inserted
replaced
7:096c6bbf4a04 | 8:844eb8c36f32 |
---|---|
48 </inputs> | 48 </inputs> |
49 <outputs> | 49 <outputs> |
50 <data format="html" name="html_file" label="riboplot (HTML report)"/> | 50 <data format="html" name="html_file" label="riboplot (HTML report)"/> |
51 </outputs> | 51 </outputs> |
52 <help> | 52 <help> |
53 **RiboPlot** | |
54 | |
55 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). | |
56 | |
57 ---- | |
58 | |
59 **Parameters** | |
60 | |
61 1. Ribo-Seq alignment file (Sorted BAM file) | |
62 | |
63 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM | |
64 file should be sorted. This can be done using one of the following methods. | |
65 | |
66 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. | |
67 2. ``samtools sort input.bam inputsorted`` | |
68 | |
69 2. Transcriptome (FASTA) | |
70 | |
71 A FASTA format file with sequences of the transcripts. | |
72 | |
73 3. Name of the transcript to plot (Text) | |
74 | |
75 The name of the transcript to plot **should** match the name in the transcriptome (FASTA) | |
76 and the Ribo-Seq/RNA-Seq alignment (BAM). | |
77 | |
78 4. RNA coverage [optional] (Sorted BAM file) | |
79 | |
80 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. | |
81 | |
82 5. Read lengths to consider [Optional] (Integer - 0 or greater) | |
83 | |
84 If this option is provided, only Ribo-Seq data of the given length is considered. | |
85 | |
86 6. Offset [optional] (Integer - 0 or greater) | |
87 | |
88 If this option is provided, this offset is added to the read alignment positions. | |
89 | |
90 ---- | |
91 | |
92 **Output** | |
93 | |
94 1. Plots (PNG and SVG) | |
95 | |
96 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) | |
97 | |
98 RNA coverage as a gray background (if the RNA coverage option was selected). | |
99 | |
100 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames. | |
101 | |
102 The color codes are start (white) and stop (dark gray). | |
103 | |
104 .. image:: images/riboplot.png | |
105 | |
106 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) | |
107 | |
53 </help> | 108 </help> |
54 </tool> | 109 </tool> |