Mercurial > repos > sblanck > mpagenomics
comparison extractCN.xml @ 4:3fcbb8030fcc draft
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author | sblanck |
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date | Mon, 12 Apr 2021 14:47:09 +0000 |
parents | 4d539083cf7f |
children | 4f753bb8681e |
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3:94fc6ed13946 | 4:3fcbb8030fcc |
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1 <tool id="extract" name="Extract" force_history_refresh="True" version="1.1.0"> | 1 <tool id="extract" name="Extract" version="1.2.0"> |
2 <description>copy number or allele B fraction signal</description> | 2 <description>copy number or allele B fraction signal</description> |
3 <requirement type="package" version="1.1.2">mpagenomics</requirement> | 3 <requirements> |
4 <command> | 4 <container type="docker">sblanck/mpagenomicsdependencies</container> |
5 </requirements> | |
6 <command> | |
5 <![CDATA[ | 7 <![CDATA[ |
6 Rscript | 8 Rscript |
7 ${__tool_directory__}/extractCN.R | 9 ${__tool_directory__}/extractCN.R |
8 --chrom '$chrom' | 10 --chrom '$chrom' |
9 --input '$input' | 11 --input '$input' |
12 --zip '$zip' | |
10 --output '$output' | 13 --output '$output' |
11 --new_file_path '$__new_file_path__' | 14 --new_file_path '$output.extra_files_path' |
12 #if $settings.settingsType == "file": | 15 #if $settings.settingsType == "file": |
13 --settings_type '$settings.inputs' | 16 --settings_type '$settings.inputs' |
14 #end if | 17 #end if |
15 #if $settings.settingsType == "dataset": | 18 #if $settings.settingsType == "dataset": |
16 --settings_type 'dataset' | 19 --settings_type 'dataset' |
17 #end if | 20 #end if |
18 #if $settingsSNP.signal == "fracB": | 21 #if $settingsSNP.signal == "fracB": |
19 --settings_snp 'TRUE' | 22 --settings_snp 'TRUE' |
20 | 23 --settings_tumor '$settingsSNP.tumorcsvFracBsym' |
21 #if $settingsSNP.sym.symmetrize=="TRUE" | 24 --symmetrize 'TRUE' |
22 --settings_tumor '$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 '$settingsSNP.sym.symmetrize' | |
31 #else | 25 #else |
32 --settings_snp '$settingsSNP.snp' | 26 --settings_snp '$settingsSNP.snp' |
33 #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard": | 27 #if $settingsSNP.settingsTumor.settingsTypeTumor == "standard": |
34 --settings_tumor 'None' | 28 --settings_tumor 'None' |
35 #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor": | 29 #elif $settingsSNP.settingsTumor.settingsTypeTumor == "tumor": |
36 --settings_tumor '$tumorcsvCN' | 30 --settings_tumor '${settingsSNP.settingsTumor.tumorcsvCN}' |
37 #end if | 31 #end if |
38 #end if | 32 #end if |
39 --outputlog '$outputlog' | 33 --outputlog '$outputlog' |
40 --log '$log' | 34 --log '$log' |
41 --settings_signal '$settingsSNP.signal' | 35 --settings_signal '$settingsSNP.signal' |
42 --userid '$__user_id__' | 36 --userid '$__user_id__' |
43 ]]> | 37 ]]> |
44 </command> | 38 </command> |
45 <inputs> | 39 <inputs> |
46 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/> | 40 <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"/> | |
47 <conditional name="settings"> | 42 <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"> | 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"> |
49 <option value="dataset">Select whole dataset</option> | 44 <option value="dataset">Select whole dataset</option> |
50 <option value="file">Select file individually</option> | 45 <option value="file">Select file individually</option> |
51 </param> | 46 </param> |
64 <param name="signal" type="select" multiple="false" label="Signal you want to work on"> | 59 <param name="signal" type="select" multiple="false" label="Signal you want to work on"> |
65 <option value="CN">CN</option> | 60 <option value="CN">CN</option> |
66 <option value="fracB">fracB</option> | 61 <option value="fracB">fracB</option> |
67 </param> | 62 </param> |
68 <when value="fracB"> | 63 <when value="fracB"> |
69 <conditional name="sym"> | 64 <!--conditional name="sym"> |
70 <param name="symmetrize" type="select" label="Symmetrize allele B signal"> | 65 <param name="symmetrize" type="select" label="Symmetrize allele B signal"> |
71 <option value="TRUE">Yes</option> | 66 <option value="TRUE">Yes</option> |
72 <option value="FALSE">No</option> | 67 <option value="FALSE">No</option> |
73 </param> | 68 </param> |
74 <when value="TRUE"> | 69 <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."/> | 70 <param name="tumorcsvFracBsym" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/> |
76 </when> | 71 <!--/when> |
77 <when value="FALSE"> | 72 <when value="FALSE"> |
78 <conditional name="settingsTumorFracB"> | 73 <conditional name="settingsTumorFracB"> |
79 <param name="settingsTypeTumorFracB" type="select" label="Reference"> | 74 <param name="settingsTypeTumorFracB" type="select" label="Reference"> |
80 <option value="standard">Study without reference</option> | 75 <option value="standard">Study without reference</option> |
81 <option value="tumor">Normal-tumor study</option> | 76 <option value="tumor">Normal-tumor study</option> |
83 <when value="standard"/> | 78 <when value="standard"/> |
84 <when value="tumor"> | 79 <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."/> | 80 <param name="tumorcsvFracB" type="data" format="csv" label="Tumor boost csv file" help="Normal-tumor csv file. See below for more information."/> |
86 </when> | 81 </when> |
87 </conditional> | 82 </conditional> |
88 </when> | 83 </when--> |
89 </conditional> | 84 <!--/conditional--> |
90 </when> | 85 </when> |
91 <when value="CN"> | 86 <when value="CN"> |
92 <conditional name="settingsTumor"> | 87 <conditional name="settingsTumor"> |
93 <param name="settingsTypeTumor" type="select" label="Reference"> | 88 <param name="settingsTypeTumor" type="select" label="Reference"> |
94 <option value="standard">Study without reference</option> | 89 <option value="standard">Study without reference</option> |
107 </conditional> | 102 </conditional> |
108 | 103 |
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" /--> | 104 <!--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 | 105 |
111 <param name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="You can select several chromosomeleave blank for all chromosomes"> | 106 <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> | 107 <option value="1">chr 1</option> |
114 <option value="2">chr 2</option> | 108 <option value="2">chr 2</option> |
115 <option value="3">chr 3</option> | 109 <option value="3">chr 3</option> |
116 <option value="4">chr 4</option> | 110 <option value="4">chr 4</option> |
117 <option value="5">chr 5</option> | 111 <option value="5">chr 5</option> |
142 <option value="TRUE">Yes</option> | 136 <option value="TRUE">Yes</option> |
143 <option value="FALSE">No</option> | 137 <option value="FALSE">No</option> |
144 </param> | 138 </param> |
145 </inputs> | 139 </inputs> |
146 <outputs> | 140 <outputs> |
147 <data format="sef" name="output" label="signal extraction of ${input.name}" /> | 141 <data format="sef" name="output" label="signal extraction of ${settingsSNP.signal} of ${input.name}" /> |
148 <data format="log" name="log" label="log of signal extraction of ${input.name}"> | 142 <data format="log" name="log" label="log of signal extraction of ${settingsSNP.signal} of ${input.name}"> |
149 <filter>outputlog == "TRUE"</filter> | 143 <filter>outputlog == "TRUE"</filter> |
150 </data> | 144 </data> |
151 </outputs> | 145 </outputs> |
152 <stdio> | 146 <stdio> |
153 <exit_code range="1:" level="fatal" description="See logs for more details" /> | 147 <exit_code range="1:" level="fatal" description="See logs for more details" /> |