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comparison extractCN.xml @ 5:4f753bb8681e draft

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"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
author sblanck
date Tue, 20 Apr 2021 13:11:24 +0000
parents 3fcbb8030fcc
children
comparison
equal deleted inserted replaced
4:3fcbb8030fcc 5:4f753bb8681e
1 <tool id="extract" name="Extract" version="1.2.0"> 1 <tool id="extract" name="Extract" version="1.3.0">
2 <description>copy number or allele B fraction signal</description> 2 <description>copy number or allele B fraction signal</description>
3 <requirements> 3 <requirements>
4 <container type="docker">sblanck/mpagenomicsdependencies</container> 4 <container type="docker">sblanck/mpagenomicsdependencies</container>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
8 Rscript 8 Rscript
9 ${__tool_directory__}/extractCN.R 9 ${__tool_directory__}/extractCN.R
10 --chrom '$chrom' 10 --chrom '$chrom'
11 --input '$input' 11 --input '$input'
12 --zip '$zip' 12 --zip '$zip'
13 --output '$output'
14 --new_file_path '$output.extra_files_path'
15 #if $settings.settingsType == "file": 13 #if $settings.settingsType == "file":
16 --settings_type '$settings.inputs' 14 --settings_type '$settings.inputs'
17 #end if 15 #end if
18 #if $settings.settingsType == "dataset": 16 #if $settings.settingsType == "dataset":
19 --settings_type 'dataset' 17 --settings_type 'dataset'
20 #end if 18 #end if
21 #if $settingsSNP.signal == "fracB": 19 #if $settingsSNP.signal == "fracB":
22 --settings_snp 'TRUE' 20 --new_file_path '$outputF.extra_files_path'
21 --output '$outputF'
22 --settings_snp 'TRUE'
23 --settings_tumor '$settingsSNP.tumorcsvFracBsym' 23 --settings_tumor '$settingsSNP.tumorcsvFracBsym'
24 --symmetrize 'TRUE' 24 --symmetrize 'TRUE'
25 #else 25 #else
26 --settings_snp '$settingsSNP.snp' 26 --new_file_path '$outputC.extra_files_path'
27 --output '$outputC'
28 --settings_snp '$settingsSNP.snp'
27 #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard": 29 #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard":
28 --settings_tumor 'None' 30 --settings_tumor 'None'
29 #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor": 31 #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor":
30 --settings_tumor '${settingsSNP.settingsTumor.tumorcsvCN}' 32 --settings_tumor '${settingsSNP.settingsTumor.tumorcsvCN}'
31 #end if 33 #end if
36 --userid '$__user_id__' 38 --userid '$__user_id__'
37 ]]> 39 ]]>
38 </command> 40 </command>
39 <inputs> 41 <inputs>
40 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/> 42 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
41 <param name="zip" type="data" format="zip" label="Zip results file" help="Zip results file generated by the Data normalization tool"/> 43 <param name="zip" type="data" format="nzip" label="Zip results file" help="Zip results file generated by the Data normalization tool"/>
42 <conditional name="settings"> 44 <conditional name="settings">
43 <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"> 45 <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">
44 <option value="dataset">Select whole dataset</option> 46 <option value="dataset">Select whole dataset</option>
45 <option value="file">Select file individually</option> 47 <option value="file">Select file individually</option>
46 </param> 48 </param>
136 <option value="TRUE">Yes</option> 138 <option value="TRUE">Yes</option>
137 <option value="FALSE">No</option> 139 <option value="FALSE">No</option>
138 </param> 140 </param>
139 </inputs> 141 </inputs>
140 <outputs> 142 <outputs>
141 <data format="sef" name="output" label="signal extraction of ${settingsSNP.signal} of ${input.name}" /> 143 <data format="saf" name="outputF" label="signal extraction of ${settingsSNP.signal} of ${input.name}">
144 <filter>settingsSNP['signal']=='fracB'</filter>
145 </data>
146
147 <data format="sef" name="outputC" label="signal extraction of ${settingsSNP.signal} of ${input.name}">
148 <filter>settingsSNP['signal']=='CN'</filter>
149 </data>
150
142 <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} of ${input.name}"> 151 <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} of ${input.name}">
143 <filter>outputlog == "TRUE"</filter> 152 <filter>outputlog == "TRUE"</filter>
144 </data> 153 </data>
145 </outputs> 154 </outputs>
146 <stdio> 155 <stdio>