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comparison XSeekerPreparator.xml @ 3:fa97d16330be draft

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" master branch Updating"
author lain
date Thu, 17 Dec 2020 10:13:58 +0000
parents eb7756ab1cbd
children 8cc9fc8eacac
comparison
equal deleted inserted replaced
2:eb7756ab1cbd 3:fa97d16330be
1 <tool id="xseeker_preparator" 1 <tool id="xseeker_preparator"
2 name="XSeeker Preparator" 2 name="XSeeker Preparator"
3 version="1.0.1" 3 version="1.0.1"
4 profile="20.04"
5 > 4 >
6 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description> 5 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
7 6
8 <edam_operations> 7 <edam_operations>
9 <edam_operation>operation_1812</edam_operation> 8 <edam_operation>operation_1812</edam_operation>
10 <edam_operation>operation_0335</edam_operation> 9 <edam_operation>operation_0335</edam_operation>
11 </edam_operations> 10 </edam_operations>
12 11
13 <requirements> 12 <requirements>
14 <requirement type="set_environment">R_SCRIPT_PATH</requirement> 13 <requirement type="set_environment">R_SCRIPT</requirement>
15 <requirement type="package" version="4.0.0">R</requirement> 14 <requirement type="package" version="4.0.0">R</requirement>
16 <requirement type="package" version="1.6.6">optparse</requirement> 15 <requirement type="package" version="1.6.6">optparse</requirement>
17 <requirement type="package" version="3.10.2">xcms</requirement> 16 <requirement type="package" version="3.10.2">xcms</requirement>
18 <requirement type="package" version="1.2.1">blob</requirement> 17 <requirement type="package" version="1.2.1">blob</requirement>
19 <requirement type="package" version="0.9.4">fst</requirement> 18 <requirement type="package" version="0.9.4">fst</requirement>
36 /> 35 />
37 36
38 </stdio> 37 </stdio>
39 38
40 <version_command> 39 <version_command>
41 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v 40 $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
42 </version_command> 41 </version_command>
43 42
44 <command> 43 <command>
45 <![CDATA[ 44 <![CDATA[
46 45 $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'
47 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
48 46
49 -P 47 -P
50 48
51 --input '$input' 49 --input '$input'
52 --output '$output' 50 --output '$output'
154 </section> 152 </section>
155 </inputs> 153 </inputs>
156 154
157 155
158 <outputs> 156 <outputs>
159 <data format="xseeker.sqlite" name="output" /> 157 <data format="sqlite" name="output" />
160 </outputs> 158 </outputs>
161 159
162 <configfiles> 160 <configfiles>
163 <configfile name="base_config"> 161 <configfile name="base_config">
164 tryCatch({ 162 tryCatch({