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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
author sblanck
date Tue, 12 May 2020 10:40:36 -0400
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1 <tool id="segFracB" name="Segmentation of allele B fraction " force_history_refresh="True" version="1.0.0">
2 <description></description>
3 <command>
4 <![CDATA[
5 Rscript
6 ${__tool_directory__}/segmentFracB.R
7 --chrom '$chrom'
8 --input '$input'
9 --output '$output'
10 --new_file_path '$__new_file_path__'
11 #if $settings.settingsType == "file":
12 --settings_type '$settings.inputs'
13 #end if
14 #if $settings.settingsType == "dataset":
15 --settings_type '$settings.settingsType'
16 #end if
17 --output_graph '$outputgraph'
18 --zip_figures '$zipfigures'
19 --settings_tumor '$tumorcsv'
20 --outputlog '$outputlog'
21 --log '$log'
22 --userid '$__user_id__'
23 --method '$method'
24 ]]>
25 </command>
26 <inputs>
27 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
28
29 <conditional name="settings">
30 <param name="settingsType" type="select" label="Files selection Mode" help="Select the whole cel files dataset or pick-up only few files from the dataset">
31 <option value="dataset">Select whole dataset</option>
32 <option value="file">Select file individually</option>
33 </param>
34 <when value="dataset" />
35 <when value="file">
36 <param name="inputs" type="select" format="cel" multiple="true" label="Cel files">
37 <options from_dataset="input">
38 <column name="name" index="0"/>
39 <column name="value" index="0"/>
40 </options>
41 </param>
42 </when>
43 </conditional>
44
45 <param name="tumorcsv" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/>
46
47
48 <!--param name="chrom" type="text" value="All" label="Chromosomes" help="Chromosomes to segment. Use comma to choose multiple chromosomes: e.g. 1, 3, 8. Use 'All' for a segmentation on all chromosomes" /-->
49
50 <param name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="leave blank for all chromosomes">
51 <option value="All">All</option>
52 <option value="1">chr 1</option>
53 <option value="2">chr 2</option>
54 <option value="3">chr 3</option>
55 <option value="4">chr 4</option>
56 <option value="5">chr 5</option>
57 <option value="6">chr 6</option>
58 <option value="7">chr 7</option>
59 <option value="8">chr 8</option>
60 <option value="9">chr 9</option>
61 <option value="10">chr 10</option>
62 <option value="11">chr 11</option>
63 <option value="12">chr 12</option>
64 <option value="13">chr 13</option>
65 <option value="14">chr 14</option>
66 <option value="15">chr 15</option>
67 <option value="16">chr 16</option>
68 <option value="17">chr 17</option>
69 <option value="18">chr 18</option>
70 <option value="19">chr 19</option>
71 <option value="20">chr 20</option>
72 <option value="21">chr 21</option>
73 <option value="22">chr 22</option>
74 <option value="23">chr 23</option>
75 <option value="24">chr 24</option>
76 <option value="25">chr 25</option>
77 </param>
78 <param name="method" type="select" label="Segmentation method" help="">
79 <option value="cghseg">cghseg</option>
80 <option value="PELT">PELT</option>
81 </param>
82 <param name="outputgraph" type="select" label="Output figures">
83 <option value="TRUE">Yes</option>
84 <option value="FALSE">No</option>
85 </param>
86 <param name="outputlog" type="select" label="Output log">
87 <option value="TRUE">Yes</option>
88 <option value="FALSE">No</option>
89 </param>
90 </inputs>
91 <outputs>
92 <data format="sar" name="output" label="allele B fraction segmentation of ${input.name}" />
93 <data format="zip" name="zipfigures" label="allele B fraction segmentation figures of ${input.name}">
94 <filter>outputgraph == "TRUE"</filter>
95 </data>
96 <data format="log" name="log" label="log of allele B fraction segmentation of ${input.name}">
97 <filter>outputlog == "TRUE"</filter>
98 </data>
99 </outputs>
100 <stdio>
101 <exit_code range="1:" level="fatal" description="See logs for more details" />
102 </stdio>
103 <help>
104 .. class:: warningmark
105
106 Data normalization must be run (with the data normalization tool) prior to segmentation.
107
108 -----
109
110 **What it does**
111 This tool segments allele B fraction extracted from the previously normalized data. This tools works only on normal-tumor study.
112
113 Outputs:
114
115 *A tabular text file containing 6 columns which describe all the segment (1 line per segment):*
116
117 - sampleNames: Name of the file.
118 - chrom: The chromosome of the segment.
119 - chromStart: The starting position (in bp) of the segment. This position is not included in the segment.
120 - chromEnd: The ending position (in bp) of the segment. This position is included in the segment.
121 - probes: Number of probes in the segment.
122 - means: Mean of the segment.
123
124 *A .zip file containing all the figures (optionnal)*
125
126 -----
127
128 **Normal-tumor csv files**
129
130 Normal-tumor csv file is required to segment Allele B fraction, because naive genotyping is based on normal samples :
131
132 - The first column contains the names of the files corresponding to normal samples of the dataset.
133
134 - The second column contains the names of the tumor samples files.
135
136 - Column names of these two columns are respectively normal and tumor.
137
138 - Columns are separated by a comma.
139
140 - *Extensions of the files (.CEL for example) should be removed*
141
142
143
144 **Example**
145
146 Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
147
148 patient1_normal.cel
149 patient1_tumor.cel
150 patient2_normal.cel
151 patient2_tumor.cel
152 patient3_normal.cel
153 patient3_tumor.cel
154
155
156 The csv file should look like this ::
157
158 normal,tumor
159 patient1_normal,patient1_tumor
160 patient2_normal,patient2_tumor
161 patient3_normal,patient3_tumor
162
163 -----
164
165
166 **Citation**
167
168 If you use this tool please cite :
169
170 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
171
172 If segmentation is performed with PELT, please cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. &lt;http://arxiv.org/abs/1101.1438&gt;`_
173
174 If segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. &lt;http://www.ncbi.nlm.nih.gov/pubmed/15705208&gt;`_ ,
175 and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. &lt;http://arxiv.org/abs/1004.0887&gt;`_
176
177 </help>
178 </tool>