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comparison metagene.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_metagene" name="Metagene Analysis" version="0.4.0">
2 <description>
3 (Step 3) Metagene analysis using riboSeqR.
4 </description>
5 <requirements>
6 <requirement type="R-module">riboSeqR</requirement>
7 </requirements>
8 <command interpreter="python">riboseqr/metagene.py
9 --rdata_load "$rdata_load"
10 --selected_lengths "$selected_lengths"
11 --selected_frames "$selected_frames"
12 --hit_mean "$hit_mean"
13 --unique_hit_mean "$unique_hit_mean"
14 --ratio_check "$ratio_check"
15 --plot_lengths "$plot_lengths"
16 --min5p "$min5p"
17 --max5p "$max5p"
18 --min3p "$min3p"
19 --max3p "$max3p"
20 --cap "$cap"
21 --plot_title "$plot_title"
22 --rdata_save "$rdata_save"
23 --html_file "$html_file"
24 --output_path "$html_file.files_path"
25 </command>
26 <inputs>
27 <param name="rdata_load" type="data" format="rda"
28 label="Select Triplet periodicity (R data file)"
29 multiple="false" optional="false"
30 help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;filterHits parameters (footprint reads to be used in the analysis)&lt;/font&gt;&lt;/h4&gt;">
31 <validator type="expression"
32 message="Please check if the correct RDA file is selected">value.name == "Triplet periodicity (R data file)"</validator>
33 </param>
34
35 <param name="selected_lengths" type="text" value="27"
36 label="Length of ribosome footprint
37 reads to be used in filtering (lengths)"
38 help="ex: 27,28. Multiple values must be comma-separated.
39 Please consult Periodicity-report.txt." optional="false">
40 <validator type="empty_field" message="Field requires a value"/>
41 </param>
42
43 <param name="selected_frames" type="text" value=""
44 label="Frames of the ribosome footprint reads to be used in filtering
45 (frames)"
46 help="ex: 1,0. Should be of equal length to the lengths parameter above.
47 Multiple values must be comma-separated.
48 Please consult the periodicity report from previous step."
49 optional="false">
50 <validator type="empty_field" message="Field requires a value"/>
51 </param>
52
53 <param name="hit_mean" size="4" type="integer" value="10"
54 label="Mean number of hits within a replicate group that
55 should be observed to pass filtering (hitMean)" optional="false">
56 <validator type="empty_field" message="Field requires a value"/>
57 </param>
58
59 <param name="unique_hit_mean" size="4" type="integer" value="1"
60 label="Mean number of unique sequences within a replicate group
61 that should be observed to pass filtering
62 (unqhitMean)" optional="false">
63 <validator type="empty_field" message="Field requires a value"/>
64 </param>
65
66 <param name="ratio_check" type="boolean" checked="yes"
67 label="Check the ratios of the expected phase to maximal phase
68 within the putative coding sequence
69 (ratioCheck)" falsevalue="FALSE"
70 truevalue="TRUE"
71 help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotCDS parameters&lt;/font&gt;&lt;/h4&gt;"/>
72
73 <param name="plot_lengths" type="text"
74 label="Length of footprints to be
75 plotted (lengths)"
76 help="Multiple values should be comma-separated.
77 In that case, multiple plots will be produced" value="27"/>
78
79 <param name="min5p" label="The distance upstream of the translation
80 start to be plotted (min5p)" value="-20" type="integer"/>
81
82 <param name="max5p" label="The distance downstream of the translation
83 start to be plotted (max5p)" value="200" type="integer"/>
84
85 <param name="min3p" label="The distance upstream of the translation
86 end to be plotted (min3p)" value="-200" type="integer"/>
87
88 <param name="max3p" label="The distance downtream of the translation
89 end to be plotted (max3p)" value="20" type="integer"/>
90
91 <param name="cap"
92 label="If given, caps the height of plotted values (cap)"
93 value="" type="integer" optional="true"/>
94
95 <param name="plot_title"
96 label="Title of the plot (main)" type="text" size="30"
97 value=""/>
98 </inputs>
99 <outputs>
100 <data format="rda" name="rdata_save"
101 label="Metagene analysis (R data file)"/>
102 <data format="html" name="html_file"
103 label="Metagene analysis (HTML report)"/>
104 </outputs>
105 <tests>
106 <test>
107 <param name="rdata_load" value="Triplet periodicity (R data file)" ftype="rda"/>
108 <param name="selected_lengths" value="28" />
109 <param name="selected_frames" value="0" />
110 <param name="plot_lengths" value="28" />
111 <output name="html_file" file="Metagene_analysis_(HTML_report).html">
112 <extra_files type="file" name="Metagene-analysis-plot1.png" value="Metagene-analysis-plot1.png"/>
113 <extra_files type="file" name="Metagene-analysis-plot1.pdf" value="Metagene-analysis-plot1.pdf"/>
114 </output>
115 </test>
116 </tests>
117 <help>
118 About
119 -----
120 Metagene analysis using riboSeqR. The input is the R data file from the previous
121 step - Triplet periodicity.
122
123 riboSeqR version: **1.0.4**.
124
125 How to use?
126 -----------
127 Inputs
128 ......
129 #. Select **Triplet periodicity (R data file)** from the previous step.
130
131 #. Specify length of ribosome footprint reads to be used in filtering
132 (lengths). Only these reads **will** be used in the analysis.
133
134 #. Specify frames to consider. This information can be obtained
135 from the **Triplet periodicity (HTML report)**.
136
137 .. class:: warningmark
138
139 Please note that the frames specified should correspond to the
140 lengths of the reads.
141
142 #. Under **plotCDS parameters**, input length of footprints to be considered for
143 generating the plot.
144
145 #. Review/change other options if necessary and execute program.
146
147 Outputs
148 .......
149 The following files will be generated on completion:
150
151 #. Metagene analysis (HTML report)
152
153 A HTML file with results and links to other output files - plots for
154 specified lengths (PDF) and R script used for the session.
155
156 #. Metagene analysis (R data file)
157
158 Used as input for the next step - *Plot Rribosome Profile*.
159
160 riboSeqR functions used
161 .......................
162 filterHits.
163
164 For detailed description of the functions and the options used, please consult
165 the riboSeqR documentation.
166
167 Links
168 .....
169 * `Bioconductor package information on riboSeqR`__
170 * riboSeqR - `Reference manual`_
171 * riboSeqR - `Introduction and workflow example`_
172
173 .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html
174
175 __ riboSeqR_
176
177 .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf
178
179 .. _`Reference manual`: manual_
180
181 .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf
182
183 .. _`Introduction and workflow example`: documentation_
184
185 </help>
186 </tool>