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comparison filter.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="callfilter" name="Filter" description="segmented and called data" version="1.2.0"> 1 <tool id="callfilter" name="Filter" description="segmented and called data" version="1.3.0">
2 <requirements> 2 <requirements>
3 <container type="docker">sblanck/mpagenomicsdependencies</container> 3 <container type="docker">sblanck/mpagenomicsdependencies</container>
4 </requirements> 4 </requirements>
5 <command> 5 <command>
6 <![CDATA[ 6 <![CDATA[
7 Rscript 7 Rscript
8 ${__tool_directory__}/filter.R 8 ${__tool_directory__}/filter.R
9 --input '$input' 9 --input '${settingsSNP.input_cond}'
10 --length '$length' 10 --length '$length'
11 --probes '$probes' 11 --probes '$probes'
12 --new_file_path '$output.extra_files_path'
13 #if $settingsSNP.signal == "fracB": 12 #if $settingsSNP.signal == "fracB":
14 --nbcall 'normal' 13 --nbcall 'normal'
15 #else 14 --output '$outputF'
15 --new_file_path '$outputF.extra_files_path'
16 #else
16 --nbcall '${settingsSNP.nbcall}' 17 --nbcall '${settingsSNP.nbcall}'
18 --output '$outputC'
19 --new_file_path '$outputC.extra_files_path'
17 20
18 #end if 21 #end if
19 --settings_signal '$settingsSNP.signal' 22 --settings_signal '$settingsSNP.signal'
20 --output '$output'
21 --outputlog '$outputlog' 23 --outputlog '$outputlog'
22 --log '$log' 24 --log '$log'
23 ]]> 25 ]]>
24 </command> 26 </command>
25 <inputs> 27 <inputs>
26 <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/> 28 <conditional name="settingsSNP">
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"/>
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"/>
29
30 <conditional name="settingsSNP">
31 <param name="signal" type="select" multiple="false" label="Signal you want to work on"> 29 <param name="signal" type="select" multiple="false" label="Signal you want to work on">
32 <option value="CN">CN</option> 30 <option value="CN">CN</option>
33 <option value="fracB">fracB</option> 31 <option value="fracB">fracB</option>
34 </param> 32 </param>
35 <when value="CN"> 33 <when value="CN">
36 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep"> 34 <param name="input_cond" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
37 <option value="double_loss">double loss</option> 35 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
38 <option value="loss">loss</option> 36 <option value="double_loss">double loss</option>
39 <option value="normal">normal</option> 37 <option value="loss">loss</option>
40 <option value="gain">gain</option> 38 <option value="normal">normal</option>
41 <option value="amplification">amplification</option> 39 <option value="gain">gain</option>
42 </param> 40 <option value="amplification">amplification</option>
43 </when> 41 </param>
42 </when>
43 <when value="fracB">
44 <param name="input_cond" type="data" format="sar" label="Segmented allele b data file" help="Input file with segments"/>
45 </when>
44 46
45 </conditional> 47 </conditional>
48
49
50 <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"/>
51 <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"/>
52
46 <param name="outputlog" type="select" label="Output log"> 53 <param name="outputlog" type="select" label="Output log">
47 <option value="TRUE">Yes</option> 54 <option value="TRUE">Yes</option>
48 <option value="FALSE">No</option> 55 <option value="FALSE">No</option>
49 </param> 56 </param>
50 </inputs> 57 </inputs>
51 58
52 <outputs> 59 <outputs>
53 <data format="tabular" name="output" label="filter of ${on_string}" /> 60 <data format="scr" name="outputC" label="filter of ${settingsSNP.input_cond.name}">
54 61 <filter>settingsSNP['signal'] == 'CN'</filter>
55 <data format="log" name="log" label="log of filter of ${input.name}"> 62 </data>
63 <data format="sar" name="outputF" label="filter of ${settingsSNP.input_cond.name}">
64 <filter>settingsSNP['signal'] == "fracB"</filter>
65 </data>
66 <data format="log" name="log" label="log of filter of ${settingsSNP.input_cond.name}">
56 <filter>outputlog == "TRUE"</filter> 67 <filter>outputlog == "TRUE"</filter>
57 </data> 68 </data>
58 </outputs> 69 </outputs>
59 70
60 <stdio> 71 <stdio>