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comparison triplet.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_triplet_periodicity" name="Triplet Periodicity"
2 version="0.4.0">
3 <description>
4 (Step 2) Plot triplet periodicity for different read lengths.
5 </description>
6 <requirements>
7 <requirement type="R-module">riboSeqR</requirement>
8 </requirements>
9 <command interpreter="python">riboseqr/triplet.py
10 --rdata_load "$rdata_load"
11 --fasta_file "$fasta_file"
12 --start_codons "$start_codons"
13 --stop_codons "$stop_codons"
14 --include_lengths "$include_lengths"
15 --analyze_plot_lengths "$analyze_plot_lengths"
16 --text_legend "$text_legend"
17 --rdata_save "$rdata_save"
18 --html_file "$html_file"
19 --output_path "$html_file.files_path"
20 </command>
21 <inputs>
22 <param name="rdata_load" type="data" format="rda"
23 label="Select prepared riboSeqR input (R data file)"
24 multiple="false" optional="false"
25 help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;findCDS
26 parameters&lt;/font&gt;&lt;/h4&gt;">
27 <validator type="expression"
28 message="Please check if the correct RDA file is selected">value.name == "Prepare riboSeqR input (R data file)"</validator>
29 </param>
30
31 <param format="fasta" name="fasta_file" type="data"
32 label="Select FASTA file of the reference transcriptome"
33 help="This Fasta file is used to find start (ATG) and
34 stop codons(TAG, TAA, TGA) in frame with one another. If no files
35 are listed, you will need to upload a FASTA file of the reference
36 transcriptome.">
37 <validator type="empty_field" message="Field requires a value"/>
38 </param>
39
40 <param name="start_codons" type="text" size="15" value="ATG"
41 label="Start codon(s) to use"
42 help="Default is ATG. Multiple values must be comma-separated.">
43 <validator type="empty_field" message="Field requires a value"/>
44 </param>
45
46 <param name="stop_codons" type="text" size="15" value="TAG, TAA, TGA"
47 label="Stop codon(s) to use"
48 help="Default is TAG, TAA, TGA. Multiple values must be comma-separated.
49 &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;frameCounting
50 parameters&lt;/font&gt;&lt;/h4&gt;">
51 <validator type="empty_field" message="Field requires a value"/>
52 </param>
53
54 <param name="include_lengths" type="text"
55 label="Lengths of ribosome footprints
56 to be included"
57 help="Here, you can specify the lengths of ribosome footprints to
58 be included in the riboData object. &lt;br&gt;For example 25:30.
59 Range, semi-colon separated. &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;readingFrame
60 parameters&lt;/font&gt;&lt;/h4&gt;" value="25:30"/>
61
62 <param name="analyze_plot_lengths" type="text"
63 label="Lengths of reads to be analysed for frame-shift, or to be plotted"
64 help="[Optional] If omitted, all lengths will be plotted.
65 &lt;br&gt;For example 26:30. Range, semi-colon separated.
66 &lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotFS
67 parameters&lt;/font&gt;&lt;/h4&gt;" value="26:30"/>
68
69 <param name="text_legend" type="text" size="30"
70 value='Frame 0, Frame 1, Frame 2'
71 label="Text for legend used in the
72 plot" help="Comma-separated values."/>
73 </inputs>
74 <outputs>
75 <data format="rda" name="rdata_save"
76 label="Triplet periodicity (R data file)"/>
77 <data format="html" name="html_file"
78 label="Triplet periodicity (HTML report)"/>
79 </outputs>
80 <tests>
81 <test>
82 <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda"/>
83 <param name="fasta_file" value="zebrafish.fasta.bz2" />
84 <param name="include_lengths" value="25:30" />
85 <param name="analyze_plot_lengths" value="26:30" />
86 <output name="html_file" file="Triplet_periodicity_(HTML_report).html">
87 <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png"/>
88 <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf"/>
89 </output>
90 </test>
91 </tests>
92 <help>
93 About
94 -----
95 This tool can be used to plot triplet periodicity for different read lengths.
96 The inputs for this program are
97
98 #. Prepare riboSeqR input (R data file) from the previous step.
99 #. FASTA format file of the reference transcriptome.
100
101 riboSeqR version: **1.0.4**.
102
103 How to use?
104 -----------
105 Inputs
106 ......
107 Select prepared R data file from the previous step.
108
109 Select FASTA format file of the reference transcriptome, review/change other
110 options if necessary and execute program.
111
112 Outputs
113 .......
114 The following files will be generated on completion:
115
116 #. Triplet periodicity (HTML report)
117
118 A HTML file with results and links to other output files - triplet
119 periodicity plot (PDF) and R script used for the session.
120
121 #. Triplet periodicity (R data file)
122
123 Used as input for the next step - *Metagene analysis*.
124
125 riboSeqR functions used
126 .......................
127 findCDS, frameCounting, readingFrame and plotFS.
128
129 For detailed description of the functions and the options used, please consult
130 the riboSeqR documentation.
131
132 Links
133 .....
134 * `Bioconductor package information on riboSeqR`__
135 * riboSeqR - `Reference manual`_
136 * riboSeqR - `Introduction and workflow example`_
137
138 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
139
140 __ riboSeqR_
141
142 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
143
144 .. _`Reference manual`: manual_
145
146 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
147
148 .. _`Introduction and workflow example`: documentation_
149
150 </help>
151 </tool>