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comparison filter.xml @ 4:3fcbb8030fcc draft

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"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="callfilter" name="Filter" description="segmented and called data" force_history_refresh="True" version="1.1.0"> 1 <tool id="callfilter" name="Filter" description="segmented and called data" version="1.2.0">
2 <requirement type="package" version="1.1.2">mpagenomics</requirement> 2 <requirements>
3 <container type="docker">sblanck/mpagenomicsdependencies</container>
4 </requirements>
3 <command> 5 <command>
4 <![CDATA[ 6 <![CDATA[
5 Rscript 7 Rscript
6 ${__tool_directory__}/filter.R 8 ${__tool_directory__}/filter.R
7 --input '$input' 9 --input '$input'
8 --length '$length' 10 --length '$length'
9 --probes '$probes' 11 --probes '$probes'
10 --new_file_path '$__new_file_path__' 12 --new_file_path '$output.extra_files_path'
11 --nbcall '$nbcall' 13 #if $settingsSNP.signal == "fracB":
12 --output '$output' 14 --nbcall 'normal'
15 #else
16 --nbcall '${settingsSNP.nbcall}'
17
18 #end if
19 --settings_signal '$settingsSNP.signal'
20 --output '$output'
13 --outputlog '$outputlog' 21 --outputlog '$outputlog'
14 --log '$log' 22 --log '$log'
15 ]]> 23 ]]>
16 </command> 24 </command>
17 <inputs> 25 <inputs>
18 <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/> 26 <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
19 <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/> 27 <param name="length" type="integer" min="1" value="1" label="Minimum length for a segment" help="minimal length (in bp) to keep in a segment"/>
20 <param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/> 28 <param name="probes" type="integer" min="1" value="1" label="Minimum probes for a segment" help="minimal number of probes to keep in a segment"/>
21 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep"> 29
22 <option value="double loss">double loss</option> 30 <conditional name="settingsSNP">
23 <option value="loss">loss</option> 31 <param name="signal" type="select" multiple="false" label="Signal you want to work on">
24 <option value="normal">normal</option> 32 <option value="CN">CN</option>
25 <option value="gain">gain</option> 33 <option value="fracB">fracB</option>
26 <option value="amplification">amplification</option> 34 </param>
27 </param> 35 <when value="CN">
36 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
37 <option value="double_loss">double loss</option>
38 <option value="loss">loss</option>
39 <option value="normal">normal</option>
40 <option value="gain">gain</option>
41 <option value="amplification">amplification</option>
42 </param>
43 </when>
44
45 </conditional>
28 <param name="outputlog" type="select" label="Output log"> 46 <param name="outputlog" type="select" label="Output log">
29 <option value="TRUE">Yes</option> 47 <option value="TRUE">Yes</option>
30 <option value="FALSE">No</option> 48 <option value="FALSE">No</option>
31 </param> 49 </param>
32 </inputs> 50 </inputs>
33 51
34 <outputs> 52 <outputs>
35 <data format="tabular" name="output" label="filter of ${on_string}" /> 53 <data format="tabular" name="output" label="filter of ${on_string}" />
36 54
37 <data format="log" name="log" label="log of segmentation of ${input.name}"> 55 <data format="log" name="log" label="log of filter of ${input.name}">
38 <filter>outputlog == "TRUE"</filter> 56 <filter>outputlog == "TRUE"</filter>
39 </data> 57 </data>
40 </outputs> 58 </outputs>
41 59
42 <stdio> 60 <stdio>