Mercurial > repos > sblanck > mpagenomics

annotate 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
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4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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1 <tool id="callfilter" name="Filter" description="segmented and called data" version="1.3.0">
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3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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2 <requirements>
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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3 <container type="docker">sblanck/mpagenomicsdependencies</container>
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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4 </requirements>
0
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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5 <command>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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6 <![CDATA[
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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7 Rscript
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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8 ${__tool_directory__}/filter.R
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9 --input '${settingsSNP.input_cond}'
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10 --length '$length'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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11 --probes '$probes'
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12 #if $settingsSNP.signal == "fracB":
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13 --nbcall 'normal'
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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14 --output '$outputF'
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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15 --new_file_path '$outputF.extra_files_path'
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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16 #else
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17 --nbcall '${settingsSNP.nbcall}'
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18 --output '$outputC'
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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19 --new_file_path '$outputC.extra_files_path'
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3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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21 #end if
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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22 --settings_signal '$settingsSNP.signal'
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23 --outputlog '$outputlog'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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24 --log '$log'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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25 ]]>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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26 </command>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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27 <inputs>
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28 <conditional name="settingsSNP">
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29 <param name="signal" type="select" multiple="false" label="Signal you want to work on">
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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30 <option value="CN">CN</option>
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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31 <option value="fracB">fracB</option>
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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32 </param>
3fcbb8030fcc "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 40eda5ea3551e8b3bae32d0a8f405fe90ef22646-dirty"
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33 <when value="CN">
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34 <param name="input_cond" type="data" format="scr" label="Segmented and called data file" help="Input file with labelled segments"/>
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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35 <param name="nbcall" type="select" multiple="true" label="Label(s) to keep">
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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36 <option value="double_loss">double loss</option>
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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37 <option value="loss">loss</option>
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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38 <option value="normal">normal</option>
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39 <option value="gain">gain</option>
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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40 <option value="amplification">amplification</option>
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41 </param>
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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42 </when>
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43 <when value="fracB">
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44 <param name="input_cond" type="data" format="sar" label="Segmented allele b data file" help="Input file with segments"/>
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45 </when>
4
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46
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47 </conditional>
5
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48
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49
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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"/>
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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"/>
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52
0
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53 <param name="outputlog" type="select" label="Output log">
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54 <option value="TRUE">Yes</option>
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55 <option value="FALSE">No</option>
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56 </param>
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57 </inputs>
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58
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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59 <outputs>
5
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60 <data format="scr" name="outputC" label="filter of ${settingsSNP.input_cond.name}">
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61 <filter>settingsSNP['signal'] == 'CN'</filter>
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62 </data>
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63 <data format="sar" name="outputF" label="filter of ${settingsSNP.input_cond.name}">
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64 <filter>settingsSNP['signal'] == "fracB"</filter>
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65 </data>
4f753bb8681e "planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 0478e809d16b674c851131bb7e583cfd59d1ad01-dirty"
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66 <data format="log" name="log" label="log of filter of ${settingsSNP.input_cond.name}">
0
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67 <filter>outputlog == "TRUE"</filter>
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68 </data>
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69 </outputs>
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70
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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71 <stdio>
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72 <exit_code range="1:" level="fatal" description="See logs for more details" />
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73 </stdio>
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74 <help>
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75
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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76 **What it does**
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77
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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78 This tool filters results obtained by the segmentation and calling tool.
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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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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80 -----
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81
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82 Input/Output file:
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83
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84 *A tabular text file containing 7 columns:*
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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85
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86 - sampleNames: Name of the file.
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87 - chrom: Chromosome of the segment.
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88 - chromStart: Starting position (in bp) of the segment. This position is not included in the segment.
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89 - chromEnd: Ending position (in bp) of the segment. This position is included in the segment.
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90 - probes: Number of probes in the segment.
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91 - means: Mean of the segment.
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92 - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”).
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93
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94 -----
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95
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96 **Citation**
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97
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98 If you use this tool please cite :
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99
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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100 `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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101
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102 </help>
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103 </tool>