Mercurial > repos > sblanck > mpagenomics

comparison filter.xml @ 0:4d539083cf7f 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 689d0d8dc899a683ee18700ef385753559850233-dirty
author sblanck
date Tue, 12 May 2020 10:40:36 -0400
parents
children 3fcbb8030fcc
comparison
equal deleted inserted replaced
-1:000000000000 0:4d539083cf7f
1 <tool id="callfilter" name="Filter" description="segmented and called data" force_history_refresh="True" version="1.1.0">
2 <requirement type="package" version="1.1.2">mpagenomics</requirement>
3 <command>
4 <![CDATA[
5 Rscript
6 ${__tool_directory__}/filter.R
7 --input '$input'
8 --length '$length'
9 --probes '$probes'
10 --new_file_path '$__new_file_path__'
11 --nbcall '$nbcall'
12 --output '$output'
13 --outputlog '$outputlog'
14 --log '$log'
15 ]]>
16 </command>
17 <inputs>
18 <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"/>
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"/>
21 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
22 <option value="double loss">double loss</option>
23 <option value="loss">loss</option>
24 <option value="normal">normal</option>
25 <option value="gain">gain</option>
26 <option value="amplification">amplification</option>
27 </param>
28 <param name="outputlog" type="select" label="Output log">
29 <option value="TRUE">Yes</option>
30 <option value="FALSE">No</option>
31 </param>
32 </inputs>
33
34 <outputs>
35 <data format="tabular" name="output" label="filter of ${on_string}" />
36
37 <data format="log" name="log" label="log of segmentation of ${input.name}">
38 <filter>outputlog == "TRUE"</filter>
39 </data>
40 </outputs>
41
42 <stdio>
43 <exit_code range="1:" level="fatal" description="See logs for more details" />
44 </stdio>
45 <help>
46
47 **What it does**
48
49 This tool filters results obtained by the segmentation and calling tool.
50
51 -----
52
53 Input/Output file:
54
55 *A tabular text file containing 7 columns:*
56
57 - sampleNames: Name of the file.
58 - chrom: Chromosome of the segment.
59 - chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
60 - chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
61 - probes: Number of probes in the segment.
62 - means: Mean of the segment.
63 - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
64
65 -----
66
67 **Citation**
68
69 If you use this tool please cite :
70
71 `Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint &lt;http://fr.arxiv.org/abs/1401.5035&gt;`_
72
73 </help>
74 </tool>