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comparison ribosome_profile.xml @ 0:e01de823e919 draft default tip

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author biotechcoder
date Fri, 01 May 2015 05:41:51 -0400
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1 <tool id="riboseqr_ribosome_profile" name="Plot Ribosome Profile"
2 version="0.4.0">
3 <description>
4 (Step 4) Plot Ribosome profile using riboSeqR.
5 </description>
6 <requirements>
7 <requirement type="R-module">riboSeqR</requirement>
8 </requirements>
9 <command interpreter="python">riboseqr/ribosome_profile.py
10 --rdata_load "$rdata_load"
11 --transcript_name "$transcript_name"
12 --transcript_length "$transcript_length"
13 --transcript_cap "$transcript_cap"
14 --html_file "$html_file"
15 --output_path "$html_file.files_path"
16 </command>
17 <inputs>
18 <param name="rdata_load" format="rda" type="data"
19 label="Select Metagene analysis (R data file)"
20 multiple="false">
21 <validator type="expression"
22 message="Please check if the correct RDA file is selected">value.name == "Metagene analysis (R data file)"</validator>
23 </param>
24
25 <param name="transcript_name" type="text" size="30"
26 label="Name of the transcript to be plotted"
27 help="Plot of ribosome footprint abundance and mRNA coverage
28 (if available) for a specific transcript.">
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
38 <param name="transcript_length" type="text"
39 label="Select Ribosome footprint length"
40 help="" value="28">
41 <validator type="expression" message="Please input a single footprint length">len(value.split(',')) == 1</validator>
42 <validator type="expression" message="Please input a single footprint length">len(value.split(' ')) == 1</validator>
43 <validator type="empty_field" message="Field requires a value"/>
44 </param>
45
46 <param name="transcript_cap" type="integer" value="200"
47 label="Cap on the largest value that will be plotted as an
48 abundance of the ribosome footprint data"/>
49 </inputs>
50 <outputs>
51 <data format="html" name="html_file"
52 label="Plot ribosome profile (HTML report)"/>
53 </outputs>
54 <tests>
55 <test>
56 <param name="rdata_load" value="Metagene analysis (R data file)" />
57 <param name="transcript_name" value="gi|31340752|ref|NM_178437.2|" />
58 <param name="transcript_length" value="28" />
59 <param name="transcript_cap" value="200" />
60 <output name="html_file" file="Plot_ribosome_profile_(HTML_report).html">
61 <extra_files type="file" name="Ribosome-profile-plot.png" value="Ribosome-profile-plot.png" ftype="png" />
62 <extra_files type="file" name="Ribosome-profile-plot.pdf" value="Ribosome-profile-plot.pdf" ftype="pdf" />
63 </output>
64 </test>
65 </tests>
66 <requirements>
67 <requirement type="R-module">riboSeqR</requirement>
68 </requirements>
69 <help>
70 About
71 -----
72 This tool can be used for generating a ribosome profile plot for a given
73 transcript. The input is the R data file from the previous
74 step - Metagene analysis.
75
76 riboSeqR version: **1.0.4**.
77
78 How to use?
79 -----------
80 Inputs
81 ......
82 Select **Metagene analysis (R data file)** from the previous step, enter name
83 of the transcript to plot, review/change parameters and execute program.
84
85 .. class:: warningmark
86
87 The transcript name should correspond to names used in SAM alignments
88 and FASTA file of the transcriptome.
89
90 Outputs
91 .......
92 The following files will be generated on completion:
93
94 Plot ribosome profile (HTML report)
95
96 A HTML file with results and links to other output files - plot for the
97 specified transcript (PDF) and R script used for the session.
98
99 riboSeqR functions used
100 .......................
101 plotTranscript.
102
103 For detailed description of the functions and the options used, please consult
104 the riboSeqR documentation.
105
106 Links
107 .....
108 * `Bioconductor package information on riboSeqR`__
109 * riboSeqR - `Reference manual`_
110 * riboSeqR - `Introduction and workflow example`_
111
112 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
113
114 __ riboSeqR_
115
116 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
117
118 .. _`Reference manual`: manual_
119
120 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
121
122 .. _`Introduction and workflow example`: documentation_
123
124 </help>
125 </tool>