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annotate ImportDataFromMatrix.xml @ 4:58052f8bc987 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 8d4651e98155855108d1c4574392d503cc04bc95
author sblanck
date Thu, 01 Mar 2018 05:22:24 -0500
parents 1024245abc70
children 3ce32282f6a4
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1 <tool id="importMatrixData" name="Import custom data" version="1.0.0">
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2
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3 <description>Quality control and normalization of a custom matrix expression data</description>
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4
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5 <requirements>
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6 <requirement type="package">bioconductor-biobase</requirement>
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7 <requirement type="package">bioconductor-geoquery</requirement>
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8 <requirement type="package">bioconductor-geometadb</requirement>
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9 <requirement type="package">bioconductor-limma</requirement>
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10 <requirement type="package">bioconductor-biobase</requirement>
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11 <requirement type="package">bioconductor-affy</requirement>
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12 <requirement type="package">bioconductor-affyplm</requirement>
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13 <requirement type="package">r-jsonlite</requirement>
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14 <requirement type="package">r-dplyr</requirement>
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15 <requirement type="package">r-optparse</requirement>
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16 </requirements>
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17
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18 <stdio>
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19 <exit_code range="1:" />
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20 <regex match="Warning" source="both" level="warning"/>
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21 </stdio>
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22
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23 <command>
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24 <![CDATA[
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25 Rscript --vanilla
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26 ${__tool_directory__}/ImportDataFromMatrix.R
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27 --input $input
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28 --normalization $normalization
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29 --conditions $conditions
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30 --annotations $annotations
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31 --rdataoutput $result_export_eset
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32 --htmloutput $result_html
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33 --htmloutputpath $result_html.files_path
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34 --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
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35 ]]>
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36 </command>
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37
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38 <inputs>
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39 <param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
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40 <param name="normalization" type="select" label="Preprocessing/normalization">
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41 <option value="quantile">quantile normalization + log2</option>
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42 <option value="log2">log2 only</option>
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43 <option value="none">none</option>
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44 </param>
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45 <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
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46 <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>
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47 </inputs>
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48
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49 <outputs>
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50 <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>
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51 <data format="html" name="result_html" label="QC result"/>
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52 </outputs>
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53
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54 <help>
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55 <![CDATA[
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56 **What it does**
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57
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58 This tool imports data stored in a tabular text file.
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59 Column titles (chip IDs) must match the IDs of the .cond file.
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60 GPL annotation code is also required to fetch annotations from GEO.
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61
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62 **Exemple**
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63
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64 Header of input tabular text file
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65 ::
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66
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67
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68 "" "GSM80460" "GSM80461" "GSM80462" "GSM80463" "GSM80464"
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69 "1007_s_at" -0.0513991525066443 0.306845500314283 0.0854246562526777 -0.142417044615852 0.0854246562526777
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70 "1053_at" -0.187707155126729 -0.488026018218199 -0.282789700980404 0.160920188181103 0.989865622866287
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71 "117_at" 0.814755482809874 -2.15842936260448 -0.125006361067033 -0.256700472111743 0.0114956388378294
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72 "121_at" -0.0558912008920451 -0.0649174766813385 0.49467161164755 -0.0892673380970874 0.113700499164728
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73 "1294_at" 0.961993677420255 -0.0320936297098533 -0.169744675832317 -0.0969617298870879 -0.181149439104566
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74 "1316_at" 0.0454429707611671 0.43616183931445 -0.766111939825723 -0.182786075741673 0.599317793698226
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75 "1405_i_at" 2.23450132056221 0.369606070031838 -1.06190243892591 -0.190997225060914 0.595503660502742
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76
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77
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78 The .cond file should look like this
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79 ::
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80
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81 GSM80460 series of 16 tumors GSM80460 OSCE-2T SERIES OF 16 TUMORS
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82 GSM80461 series of 16 tumors GSM80461 OSCE-4T Series of 16 Tumors
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83 GSM80462 series of 16 tumors GSM80462 OSCE-6T Series of 16 Tumors
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84 GSM80476 series of 4 normals GSM80476 OSCE-2N Series of 4 Normals
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85 GSM80477 series of 4 normals GSM80477 OSCE-9N Series of 4 Normals
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86
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87
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88 **Results**
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89 - Boxplots and MA plots
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90 - Rdata object containing the data for further analysis.
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91 ]]>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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92 </help>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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93
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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94 </tool>