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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="extract" name="Extract" force_history_refresh="True" version="1.1.0">
2 <description>copy number or allele B fraction signal</description>
3 <requirement type="package" version="1.1.2">mpagenomics</requirement>
4 <command>
5 <![CDATA[
6 Rscript
7 ${__tool_directory__}/extractCN.R
8 --chrom '$chrom'
9 --input '$input'
10 --output '$output'
11 --new_file_path '$__new_file_path__'
12 #if $settings.settingsType == "file":
13 --settings_type '$settings.inputs'
14 #end if
15 #if $settings.settingsType == "dataset":
16 --settings_type 'dataset'
17 #end if
18 #if $settingsSNP.signal == "fracB":
19 --settings_snp 'TRUE'
20
21 #if $settingsSNP.sym.symmetrize=="TRUE"
22 --settings_tumor '$tumorcsvFracBsym'
23 #elif $settingsSNP.sym.symmetrize=="FALSE"
24 #if $settingsSNP.sym.settingsTumorFracB.settingsTypeTumorFracB == "standard":
25 --settings_tumor 'None'
26 #elif $settingsSNP.sym.settingsTumorFracB.settingsTypeTumorFracB == "tumor":
27 --settings_tumor '$tumorcsvFracB'
28 #end if
29 #end if
30 --symmetrize '$settingsSNP.sym.symmetrize'
31 #else
32 --settings_snp '$settingsSNP.snp'
33 #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard":
34 --settings_tumor 'None'
35 #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor":
36 --settings_tumor '$tumorcsvCN'
37 #end if
38 #end if
39 --outputlog '$outputlog'
40 --log '$log'
41 --settings_signal '$settingsSNP.signal'
42 --userid '$__user_id__'
43 ]]>
44 </command>
45 <inputs>
46 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
47 <conditional name="settings">
48 <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">
49 <option value="dataset">Select whole dataset</option>
50 <option value="file">Select file individually</option>
51 </param>
52 <when value="dataset"/>
53 <when value="file">
54 <param name="inputs" type="select" format="cel" multiple="true" label="Cel files">
55 <options from_dataset="input">
56 <column name="name" index="0"/>
57 <column name="value" index="0"/>
58 </options>
59 </param>
60 </when>
61 </conditional>
62
63 <conditional name="settingsSNP">
64 <param name="signal" type="select" multiple="false" label="Signal you want to work on">
65 <option value="CN">CN</option>
66 <option value="fracB">fracB</option>
67 </param>
68 <when value="fracB">
69 <conditional name="sym">
70 <param name="symmetrize" type="select" label="Symmetrize allele B signal">
71 <option value="TRUE">Yes</option>
72 <option value="FALSE">No</option>
73 </param>
74 <when value="TRUE">
75 <param name="tumorcsvFracBsym" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/>
76 </when>
77 <when value="FALSE">
78 <conditional name="settingsTumorFracB">
79 <param name="settingsTypeTumorFracB" type="select" label="Reference">
80 <option value="standard">Study without reference</option>
81 <option value="tumor">Normal-tumor study</option>
82 </param>
83 <when value="standard"/>
84 <when value="tumor">
85 <param name="tumorcsvFracB" type="data" format="csv" label="Tumor boost csv file" help="Normal-tumor csv file. See below for more information."/>
86 </when>
87 </conditional>
88 </when>
89 </conditional>
90 </when>
91 <when value="CN">
92 <conditional name="settingsTumor">
93 <param name="settingsTypeTumor" type="select" label="Reference">
94 <option value="standard">Study without reference</option>
95 <option value="tumor">Normal-tumor study</option>
96 </param>
97 <when value="standard"/>
98 <when value="tumor">
99 <param name="tumorcsvCN" type="data" format="csv" label="Normal tumor csv file" help="Normal-tumor csv file. See below for more information."/>
100 </when>
101 </conditional>
102 <param name="snp" type="select" label="Select Probes">
103 <option value="FALSE">CN and SNP probes</option>
104 <option value="TRUE">Only SNP probes</option>
105 </param>
106 </when>
107 </conditional>
108
109 <!--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" /-->
110
111 <param name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="You can select several chromosomeleave blank for all chromosomes">
112 <option value="All">All</option>
113 <option value="1">chr 1</option>
114 <option value="2">chr 2</option>
115 <option value="3">chr 3</option>
116 <option value="4">chr 4</option>
117 <option value="5">chr 5</option>
118 <option value="6">chr 6</option>
119 <option value="7">chr 7</option>
120 <option value="8">chr 8</option>
121 <option value="9">chr 9</option>
122 <option value="10">chr 10</option>
123 <option value="11">chr 11</option>
124 <option value="12">chr 12</option>
125 <option value="13">chr 13</option>
126 <option value="14">chr 14</option>
127 <option value="15">chr 15</option>
128 <option value="16">chr 16</option>
129 <option value="17">chr 17</option>
130 <option value="18">chr 18</option>
131 <option value="19">chr 19</option>
132 <option value="20">chr 20</option>
133 <option value="21">chr 21</option>
134 <option value="22">chr 22</option>
135 <option value="23">chr 23</option>
136 <option value="24">chr 24</option>
137 <option value="25">chr 25</option>
138
139 </param>
140
141 <param name="outputlog" type="select" label="Output log">
142 <option value="TRUE">Yes</option>
143 <option value="FALSE">No</option>
144 </param>
145 </inputs>
146 <outputs>
147 <data format="sef" name="output" label="signal extraction of ${input.name}" />
148 <data format="log" name="log" label="log of signal extraction of ${input.name}">
149 <filter>outputlog == "TRUE"</filter>
150 </data>
151 </outputs>
152 <stdio>
153 <exit_code range="1:" level="fatal" description="See logs for more details" />
154 </stdio>
155 <help>
156 .. class:: warningmark
157
158 Data normalization must be run (with the data normalization tool) prior to signal extraction.
159
160 -----
161
162 **What it does**
163 This tool extracts the copy number profile from the normalized data.
164
165 Outputs:
166
167 *A tabular text file containing 3 fixed columns and 1 column per sample:*
168
169 - chr: Chromosome.
170 - position: Genomic position (in bp).
171 - probeNames: Name of the probes of the microarray.
172 - One column per sample which contains the copy number profile for each sample.
173
174 -----
175
176 **Normal-tumor study**
177
178 In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided :
179
180 - The first column contains the names of the files corresponding to normal samples of the dataset.
181
182 - The second column contains the names of the tumor samples files.
183
184 - Column names of these two columns are respectively normal and tumor.
185
186 - Columns are separated by a comma.
187
188 - *Extensions of the files (.CEL for example) should be removed*
189
190
191
192 **Example**
193
194 Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
195
196 patient1_normal.cel
197 patient1_tumor.cel
198 patient2_normal.cel
199 patient2_tumor.cel
200 patient3_normal.cel
201 patient3_tumor.cel
202
203
204 The csv file should look like this ::
205
206 normal,tumor
207 patient1_normal,patient1_tumor
208 patient2_normal,patient2_tumor
209 patient3_normal,patient3_tumor
210
211 -----
212
213
214 **Citation**
215
216 If you use this tool please cite :
217
218 `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;`_
219
220
221 </help>
222 </tool>