Mercurial > repos > sblanck > mpagenomics

annotate segmentFracB.xml @ 2:b0346f5e9e45 draft

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planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 7679c75b4a95df45311603e2dceda55b159ffb4b-dirty
author sblanck
date Fri, 29 May 2020 10:48:28 -0400
parents 4d539083cf7f
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4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
sblanck
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1 <tool id="segFracB" name="Segmentation of allele B fraction " force_history_refresh="True" version="1.0.0">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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2 <description></description>
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3 <command>
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4 <![CDATA[
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5 Rscript
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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6 ${__tool_directory__}/segmentFracB.R
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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7 --chrom '$chrom'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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8 --input '$input'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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9 --output '$output'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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10 --new_file_path '$__new_file_path__'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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11 #if $settings.settingsType == "file":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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12 --settings_type '$settings.inputs'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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13 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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14 #if $settings.settingsType == "dataset":
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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15 --settings_type '$settings.settingsType'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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16 #end if
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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17 --output_graph '$outputgraph'
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18 --zip_figures '$zipfigures'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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19 --settings_tumor '$tumorcsv'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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20 --outputlog '$outputlog'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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21 --log '$log'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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22 --userid '$__user_id__'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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23 --method '$method'
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="dsf" label="Dataset summary file" help="Summary text file generated by the Data normalization tool"/>
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28
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29 <conditional name="settings">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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30 <param name="settingsType" type="select" label="Files selection Mode" help="Select the whole cel files dataset or pick-up only few files from the dataset">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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31 <option value="dataset">Select whole dataset</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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32 <option value="file">Select file individually</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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33 </param>
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34 <when value="dataset" />
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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35 <when value="file">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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36 <param name="inputs" type="select" format="cel" multiple="true" label="Cel files">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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37 <options from_dataset="input">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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38 <column name="name" index="0"/>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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39 <column name="value" index="0"/>
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40 </options>
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41 </param>
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42 </when>
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43 </conditional>
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44
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45 <param name="tumorcsv" type="data" format="csv" label="Normal-tumor csv file" help="Normal-tumor csv file. See below for more information."/>
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46
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47
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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48 <!--param name="chrom" type="text" value="All" label="Chromosomes" help="Chromosomes to segment. Use comma to choose multiple chromosomes: e.g. 1, 3, 8. Use 'All' for a segmentation on all chromosomes" /-->
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49
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50 <param name="chrom" type="select" size="6" multiple="true" label="Chromosomes" help="leave blank for all chromosomes">
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51 <option value="All">All</option>
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52 <option value="1">chr 1</option>
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53 <option value="2">chr 2</option>
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54 <option value="3">chr 3</option>
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55 <option value="4">chr 4</option>
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56 <option value="5">chr 5</option>
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57 <option value="6">chr 6</option>
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58 <option value="7">chr 7</option>
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59 <option value="8">chr 8</option>
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60 <option value="9">chr 9</option>
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61 <option value="10">chr 10</option>
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62 <option value="11">chr 11</option>
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63 <option value="12">chr 12</option>
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64 <option value="13">chr 13</option>
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65 <option value="14">chr 14</option>
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66 <option value="15">chr 15</option>
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67 <option value="16">chr 16</option>
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68 <option value="17">chr 17</option>
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69 <option value="18">chr 18</option>
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70 <option value="19">chr 19</option>
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71 <option value="20">chr 20</option>
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72 <option value="21">chr 21</option>
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73 <option value="22">chr 22</option>
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74 <option value="23">chr 23</option>
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75 <option value="24">chr 24</option>
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76 <option value="25">chr 25</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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77 </param>
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78 <param name="method" type="select" label="Segmentation method" help="">
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79 <option value="cghseg">cghseg</option>
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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80 <option value="PELT">PELT</option>
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81 </param>
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82 <param name="outputgraph" type="select" label="Output figures">
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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83 <option value="TRUE">Yes</option>
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84 <option value="FALSE">No</option>
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85 </param>
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86 <param name="outputlog" type="select" label="Output log">
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87 <option value="TRUE">Yes</option>
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88 <option value="FALSE">No</option>
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89 </param>
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90 </inputs>
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91 <outputs>
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92 <data format="sar" name="output" label="allele B fraction 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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93 <data format="zip" name="zipfigures" label="allele B fraction segmentation figures of ${input.name}">
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94 <filter>outputgraph == "TRUE"</filter>
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95 </data>
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96 <data format="log" name="log" label="log of allele B fraction segmentation of ${input.name}">
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97 <filter>outputlog == "TRUE"</filter>
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98 </data>
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99 </outputs>
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100 <stdio>
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101 <exit_code range="1:" level="fatal" description="See logs for more details" />
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102 </stdio>
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103 <help>
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104 .. class:: warningmark
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105
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106 Data normalization must be run (with the data normalization tool) prior to segmentation.
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107
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108 -----
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109
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110 **What it does**
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111 This tool segments allele B fraction extracted from the previously normalized data. This tools works only on normal-tumor study.
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112
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113 Outputs:
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114
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115 *A tabular text file containing 6 columns which describe all the segment (1 line per segment):*
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116
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117 - sampleNames: Name of the file.
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118 - chrom: The chromosome of the segment.
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119 - chromStart: The 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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120 - chromEnd: The 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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121 - probes: Number of probes in the segment.
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122 - means: Mean of the segment.
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123
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124 *A .zip file containing all the figures (optionnal)*
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125
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126 -----
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127
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128 **Normal-tumor csv files**
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129
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130 Normal-tumor csv file is required to segment Allele B fraction, because naive genotyping is based on normal samples :
4d539083cf7f planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty
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131
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132 - The first column contains the names of the files corresponding to normal samples of the dataset.
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133
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134 - The second column contains the names of the tumor samples files.
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135
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136 - Column names of these two columns are respectively normal and tumor.
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137
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138 - Columns are separated by a comma.
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139
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140 - *Extensions of the files (.CEL for example) should be removed*
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141
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142
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143
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144 **Example**
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145
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146 Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) ::
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147
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148 patient1_normal.cel
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149 patient1_tumor.cel
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150 patient2_normal.cel
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151 patient2_tumor.cel
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152 patient3_normal.cel
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153 patient3_tumor.cel
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154
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155
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156 The csv file should look like this ::
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157
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158 normal,tumor
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159 patient1_normal,patient1_tumor
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160 patient2_normal,patient2_tumor
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161 patient3_normal,patient3_tumor
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162
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163 -----
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164
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165
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166 **Citation**
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167
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168 If you use this tool please cite :
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169
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170 `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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172 If segmentation is performed with PELT, please cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. &lt;http://arxiv.org/abs/1101.1438&gt;`_
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173
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174 If segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. &lt;http://www.ncbi.nlm.nih.gov/pubmed/15705208&gt;`_ ,
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175 and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. &lt;http://arxiv.org/abs/1004.0887&gt;`_
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177 </help>
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178 </tool>