Mercurial > repos > sblanck > mpagenomics

comparison extractCN.xml @ 4:3fcbb8030fcc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
author sblanck
date Mon, 12 Apr 2021 14:47:09 +0000
parents 4d539083cf7f
children 4f753bb8681e
comparison
equal deleted inserted replaced
3:94fc6ed13946 4:3fcbb8030fcc
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" />