Mercurial > repos > sblanck > mpagenomics
comparison filter.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="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> |