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annotate filter.xml @ 0:4d539083cf7f draft

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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
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4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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1 <tool id="callfilter" name="Filter" description="segmented and called data" force_history_refresh="True" version="1.1.0">
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2 <requirement type="package" version="1.1.2">mpagenomics</requirement>
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3 <command>
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4 <![CDATA[
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5 Rscript
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6 ${__tool_directory__}/filter.R
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7 --input '$input'
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8 --length '$length'
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9 --probes '$probes'
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10 --new_file_path '$__new_file_path__'
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11 --nbcall '$nbcall'
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12 --output '$output'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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13 --outputlog '$outputlog'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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14 --log '$log'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="input" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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"/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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"/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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21 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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22 <option value="double loss">double loss</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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23 <option value="loss">loss</option>
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24 <option value="normal">normal</option>
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25 <option value="gain">gain</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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26 <option value="amplification">amplification</option>
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27 </param>
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28 <param name="outputlog" type="select" label="Output log">
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29 <option value="TRUE">Yes</option>
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30 <option value="FALSE">No</option>
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31 </param>
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32 </inputs>
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33
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34 <outputs>
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35 <data format="tabular" name="output" label="filter of ${on_string}" />
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36
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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37 <data format="log" name="log" label="log of segmentation of ${input.name}">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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38 <filter>outputlog == "TRUE"</filter>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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39 </data>
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40 </outputs>
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41
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42 <stdio>
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43 <exit_code range="1:" level="fatal" description="See logs for more details" />
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44 </stdio>
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45 <help>
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46
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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47 **What it does**
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48
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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49 This tool filters results obtained by the segmentation and calling tool.
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50
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51 -----
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52
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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53 Input/Output file:
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54
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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55 *A tabular text file containing 7 columns:*
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56
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57 - sampleNames: Name of the file.
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58 - chrom: Chromosome of the segment.
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59 - chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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60 - chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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61 - probes: Number of probes in the segment.
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62 - means: Mean of the segment.
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63 - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
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64
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65 -----
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67 **Citation**
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69 If you use this tool please cite :
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4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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;`_
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73 </help>
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74 </tool>