Mercurial > repos > proteore > proteore_ms_observation_pepatlas

annotate Get_ms-ms_observations.xml @ 10:ef723082fc54 draft default tip

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"planemo upload commit b061341e1157cccd90e33b945bc17705880b3e57"
author proteore
date Mon, 04 May 2020 03:29:36 -0400
parents 8fdde324e99e
children
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1 <tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2020.04.30">
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2 <description>[Human Peptide Atlas]</description>
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3 <requirements>
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4 <requirement type="package" version="3.6.1">r-base</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command interpreter="Rscript">
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10 $__tool_directory__/Get_ms-ms_observations.R
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11 --input_type="$input.ids"
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12 #if $input.ids == "list"
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13 --input="$input.list"
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14 #else
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15 --input="$input.file"
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16 --column_number="$input.ncol"
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17 --header="$input.header"
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18 #end if
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19 --atlas=${",".join([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($atlas).split(",")])}
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20 --output="$output"
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21 </command>
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22
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23 <inputs>
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24 <conditional name="input" >
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25 <param name="ids" type="select" label="Enter your IDs (UniProt Accession number only)" help="Copy/paste or from a file (e.g. table)" >
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26 <option value="list">Copy/paste your IDs</option>
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27 <option value="file" selected="true">Input file containing your IDs </option>
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28 </param>
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29 <when value="list" >
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30 <param name="list" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
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31 <sanitizer>
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32 <valid initial="string.printable">
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33 <remove value="&apos;"/>
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34 </valid>
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35 <mapping initial="none">
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36 <add source="&apos;" target="__sq__"/>
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37 </mapping>
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38 </sanitizer>
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39 </param>
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40 </when>
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41 <when value="file" >
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42 <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
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43 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
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44 <param name="ncol" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
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45 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
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46 </param>
2
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47 </when>
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48 </conditional>
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49 <!-- Peptide Atlas options -->
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50 <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
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51 <options from_data_table="proteore_peptide_atlas">
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52 <filter type="sort_by" column="2"/>
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53 </options>
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54 </param>
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55 </inputs>
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56
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57 <outputs>
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58 <data name="output" format="tsv" label=""/>
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <conditional name="input">
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64 <param name="ids" value="file"/>
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65 <param name="file" value="FKW_Lacombe_et_al_2017_OK.txt"/>
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66 <param name="ncol" value="c1"/>
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67 <param name="header" value="true"/>
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68 </conditional>
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69
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70 <!--${__HERE__} does not work here, you must put absolute path here and in test-data/peptide_atlas.loc -->
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71 <param name="atlas" value="${__HERE__}/test-data/Human_Brain_18-07-2018.tsv"/>
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72
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73 <output name="output" file="PeptideAtlas_output.txt"/>
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74 </test>
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75 </tests>
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76
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77 <help><![CDATA[
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78
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79 **Description**
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80
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81 Given a list of Uniprot accession number this tool indicates the number of times a protein has(ve) been observed in a given sample using LC-MS/MS proteomics approach.
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82 Could be of interest for people who wants to know to what extent a protein is detectable (and to roughly estimate its level) in a given sample using MS-based proteomics.
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83
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84 ----
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85
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86 **Input**
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87
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88 A list of Uniprot accession number (e.g. Q12860) provided either in a copy/paste mode or in the form of a file (in this case, it is necessary to specify the column where are your Uniprot accession number).
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89
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90 If your input file or list contains other type of IDs, please use the ID_Converter tool.
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91
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92 .. class:: warningmark
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93
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94 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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95
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96 ----
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97
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98 **Parameters**
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99
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100 "Proteomics dataset (biological sample - date of downloading)": available human biological samples (tissue/organ/body fluid) analyzed by MS/MS and processed by Peptide Atlas are the following: adrenal gland, brain, breast, CSF (cerebrospinal fluid), colon cancer, digestive system, female and male reproductive system, heart, kidney, liver, lung, pancreas, plasma (non-glycosylated), spleen, testis, urinary bladder, urine.
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101
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102 ----
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103
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104 **Output**
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105
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106 Additional columns are created for each selected proteomics sample reporting the total number of observation (called "ProteinProphet-adjusted N Obs") of all peptides detected by LC-MS/MS and assigned to a protein according to Peptide Atlas.
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107
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108 a “NA” means that no information has been reported suggesting that this protein has not been observed in the sample of interest.
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109
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110 ----
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111
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112 **Data source (release date)**
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113
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114 Data source (release date)" - replace "MS/MS Proteomics dataset (also called "build") were retrieved from Peptide Atlas website through their query interface (in January 2019) with name and release date as follow:
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115
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116 - Human Adrenal Gland 2014-08
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117 - Human Brain 2015-01
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118 - Human Breast 2014-08
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119 - Human CSF 2014-09
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120 - Human Colon Cancer 2013-02
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121 - Human Digestive System 2014-08
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122 - Human Female Reproductive System 2014-08
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123 - Human Heart 2014-08
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124 - Human Kidney 2014-08
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125 - Human Liver 2014-08
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126 - Human Lung 2014-08
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127 - Human Male Reproductive System 2014-08
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128 - Human Pancreas 2014-08
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129 - Human Plasma Non-Glyco 2017-04
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130 - Human Spleen 2014-08
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131 - Human Testis 2017-01
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132 - Human Urinary Bladder 2014-08
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133 - Human Urine 2014-08
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134
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135 ----
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136
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137 .. class:: infomark
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138
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139 **Authors**
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140
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141 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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142
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143 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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144
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145 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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146
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147 Help: contact@proteore.org for any questions or concerns about this tool.
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148
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149 ]]></help>
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150 <citations>
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151 </citations>
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152 </tool>
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153