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author biotechcoder
date Fri, 01 May 2015 05:41:51 -0400
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1 <tool id="riboseqr_prepare_input" name="Prepare riboSeqR input" version="0.4.0">
2 <description>
3 (Step 1) Prepare alignment file (SAM format, Ribo-Seq or RNA-Seq alignments)
4 for riboSeqR analysis.
5 </description>
6 <requirements>
7 <requirement type="R-module">riboSeqR</requirement>
8 </requirements>
9 <command interpreter="python">riboseqr/prepare.py
10 #set $files_ribo = []
11 #set $files_rna = []
12 #set $replicates = []
13
14 #for $i, $s in enumerate($rnaseq.datasets)
15 #silent $replicates.append($s.replicate_name.value)
16 #silent $files_ribo.append($s.ribo_files.file_name)
17 #try:
18 #silent $s.rna_files
19 #except:
20 #pass
21 #else:
22 #silent $files_rna.append($s.rna_files.file_name)
23 #end try
24 #end for
25
26 #set $ribofiles = ", ".join($files_ribo)
27 #set $rnafiles = ", ".join($files_rna)
28 #set $replicate_names = ", ".join($replicates)
29
30 --ribo_files "$ribofiles"
31 --rna_files "$rnafiles"
32 --replicate_names "$replicate_names"
33 --seqnames "$seqnames"
34 --rdata_save "$rdata_save"
35 --sam_format
36 --html_file "$html_file"
37 --output_path "$html_file.files_path"
38 </command>
39 <inputs>
40 <conditional name="rnaseq">
41 <param name="have-rnaseq" type="boolean" truevalue="checked"
42 falsevalue="unchecked" label="Have RNA-Seq data?"/>
43 <when value="checked">
44 <repeat name="datasets" title="Ribo and RNA-Seq alignment"
45 default="1">
46 <param type="text" name="replicate_name" size="20"
47 label="Provide a common name for each replicate group"
48 value=""/>
49 <param format="sam" name="ribo_files" type="data"
50 label="Ribo-Seq alignment file (SAM)"
51 multiple="false"/>
52 <param format="sam" name="rna_files" type="data"
53 label="RNA-Seq alignment file (SAM)"
54 multiple="false"/>
55 </repeat>
56 </when>
57 <when value="unchecked">
58 <repeat name="datasets" title="Ribo-Seq alignment" default="1">
59 <param type="text" name="replicate_name" size="20"
60 label="Provide a common name for each replicate group"
61 value=""/>
62 <param format="sam" name="ribo_files" type="data"
63 label="Ribo-Seq alignment file (SAM)"
64 multiple="false">
65 </param>
66 </repeat>
67 </when>
68 </conditional>
69 <param name="seqnames" type="text" area="True" label="Transcript (seqname)
70 names to be read" size="3x60"
71 help="[Optional] - only the mapped footprints for these transcripts will be
72 used in further riboSeqR analysis. Multiple transcript names should
73 be separated by commas. There should be no quotes around transcript names.">
74 <sanitizer>
75 <valid>
76 <add value="|"/>
77 </valid>
78 </sanitizer>
79 </param>
80 </inputs>
81 <outputs>
82 <data format="rda" name="rdata_save"
83 label="Prepare riboSeqR input (R data file)"/>
84 <data format="html" name="html_file"
85 label="Prepare riboSeqR input (HTML report)"/>
86 </outputs>
87 <tests>
88 <test>
89 <param name="ribo_files" value="12hRPF.sam" />
90 <output name="html_file" file="Prepare_riboSeqR_input_(HTML_report).html">
91 <extra_files type="file" name="RiboSeq file 1" value="RiboSeq file 1"/>
92 </output>
93 </test>
94 </tests>
95 <help>
96 About
97 -----
98 This tool can be used to prepare input data for riboSeqR from SAM
99 format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can
100 do this alignment manually using bowtie or the
101 "Transcriptome Mapping" -> "Align to transcriptome using Bowtie"
102 tool on RiboGalaxy_
103
104 The required input format for riboSeqR_ is mentioned in the
105 **"Getting Data"** section of the documentation_.
106
107 riboSeqR version: **1.0.4**.
108
109 How to use?
110 -----------
111 Inputs
112 ......
113 Select SAM format Ribo-Seq alignment files in the input section.
114
115 If you have RNA-Seq data, these can be included if the **"Have RNA-Seq data"**
116 option is checked.
117
118 Outputs
119 .......
120 The following files will be generated on completion:
121
122 #. Prepare riboSeqR input (HTML report) - A HTML file with links to all other
123 output files.
124
125 * Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
126 These files are plain text and lines have the following information -
127 strand, transcript name, alignment position, sequence.
128
129 Please note the alignments are made **0-indexed**.
130
131 * R script used in this session.
132
133 #. Prepare riboSeqR input (R data file) - used as input for the next step -
134 *Triplet Periodicity*.
135
136 How are the SAM alignments processed?
137 .....................................
138 #. Lines starting with ``@`` are ignored.
139 #. Lines having a ``FLAG=0`` are considered as successful alignments. These are
140 considered for the next step.
141 #. Alignment start is located on ``column 4``. These are decremented by
142 1 as SAM alignments are 1-indexed.
143 #. riboSeqR input file is written with the strand (``+``), transcript name,
144 alignment start and the aligned sequence.
145
146 riboSeqR functions used
147 .......................
148 readRibodata.
149
150 For detailed description of the functions and the options used, please consult
151 the riboSeqR documentation.
152
153 Links
154 .....
155 * `Bioconductor package information on riboSeqR`__
156 * riboSeqR - `Reference manual`_
157 * riboSeqR - `Introduction and workflow example`_
158
159 .. _RiboGalaxy: http://ribogalaxy.ucc.ie
160
161 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
162
163 __ riboSeqR_
164
165 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
166
167 .. _`Reference manual`: manual_
168
169 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
170
171 .. _`Introduction and workflow example`: documentation_
172
173 </help>
174 </tool>