Mercurial > repos > proteore > proteore_get_expression_profiles

annotate get_expression_profiles.xml @ 0:1c9562e9ea67 draft default tip

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planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
author proteore
date Thu, 13 Dec 2018 04:06:48 -0500
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1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2018.12.12">
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2 <description>by (normal or tumor) tissue/cell type [Human Protein Atlas]
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3 </description>
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4 <requirements>
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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 $__tool_directory__/get_expression_profiles.R
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11 --ref_file="$__tool_directory__/$options.proteinatlas"
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12 --input_type="$input.ids"
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13 #if $input.ids == "list"
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14 --input="$input.list"
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15 #else
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16 --input="$input.file"
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17 --column_number="$input.ncol"
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18 --header="$input.header"
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19 #end if
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20
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21 #if $options.database == "normal"
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22 --atlas="normal"
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23 --tissue="$options.normal_tissue"
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24 --level="$options.level"
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25 --reliability="$options.reliability"
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26 #else if $options.database == "tumor"
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27 --atlas="cancer"
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28 --cancer="$options.cancer_tissue"
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29 #end if
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30 --not_mapped="$not_mapped"
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31 --output="$hpa_output"
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32 </command>
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33 <inputs>
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34 <conditional name="input" >
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35 <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
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36 <option value="list">Copy/paste your identifiers</option>
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37 <option value="file" selected="true">Input file containing your identifiers</option>
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38 </param>
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39 <when value="list" >
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40 <param name="list" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: ENSG00000174876 ENSG00000178372 ENSG00000159763' >
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41 <sanitizer>
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42 <valid initial="string.printable">
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43 <remove value="&apos;"/>
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44 </valid>
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45 <mapping initial="none">
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46 <add source="&apos;" target="__sq__"/>
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47 </mapping>
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48 </sanitizer>
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49 </param>
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50 </when>
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51 <when value="file" >
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52 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of ENSG IDs" help="" />
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53 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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54 <param name="ncol" type="text" value="c1" label="The column number of ENSG IDs to map" 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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55 </when>
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56 </conditional>
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57 <conditional name="options">
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58 <param name="database" type="select" label="Human Protein Atlas (data from normal or tumor tissue)">
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59 <option value="normal">Human Normal Tissue</option>
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60 <option value="tumor">Human Tumor Tissue</option>
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61 </param>
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62 <when value="normal">
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63 <param name="proteinatlas" type="select" label="Human Protein Atlas" >
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64 <!--options from_file="proteinatlas.loc" >
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65 <column name="name" index="1"/>
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66 <column name="value" index="2"/>
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67 <filter type="remove_value" key="name" value="Full Human Protein Atlas (23/10/18)"/>
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68 <filter type="remove_value" key="name" value="HPA Tumor Tissue (23/10/18)"/>
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69 </options-->
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70 <option value="tool-data/HPA_normal_tissue_23-10-2018.tsv">HPA Normal Tissue (23/10/18)</option>
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71 </param>
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72 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False">
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73 <option value="adrenal gland" >Adrenal gland</option>
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74 <option value="appendix" >Appendix</option>
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75 <option value="bone marrow" >Bone marrow</option>
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76 <option value="breast" >Breast</option>
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77 <option value="bronchus" >Bronchus</option>
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78 <option value="caudate" >Caudate</option>
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79 <option value="cerebellum" >Cerebellum</option>
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80 <option value="cerebral cortex" >Cerebral cortex</option>
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81 <option value="cervix" >Cervix</option>
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82 <option value="colon" >Colon</option>
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83 <option value="duodenum" >Duodenum</option>
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84 <option value="endometrium 1" >Endometrium 1</option>
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85 <option value="endometrium 2" >Endometrium 2</option>
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86 <option value="epididymis" >Epididymis</option>
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87 <option value="esophagus" >Esophagus</option>
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88 <option value="fallopian tube" >Fallopian tube</option>
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89 <option value="gallbladder" >Gallbladder</option>
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90 <option value="heart muscle" >Heart muscle</option>
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91 <option value="hippocampus" >Hippocampus</option>
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92 <option value="kidney" >Kidney</option>
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93 <option value="liver" >Liver</option>
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94 <option value="lung" >Lung</option>
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95 <option value="lymph node" >Lymph node</option>
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96 <option value="nasopharynx" >Nasopharynx</option>
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97 <option value="oral mucosa" >Oral mucosa</option>
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98 <option value="ovary" >Ovary</option>
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99 <option value="pancreas" >Pancreas</option>
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100 <option value="parathyroid gland" >Parathyroid gland</option>
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101 <option value="placenta" >Placenta</option>
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102 <option value="prostate" >Prostate</option>
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103 <option value="rectum" >Rectum</option>
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104 <option value="salivary gland" >Salivary gland</option>
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105 <option value="seminal vesicle" >Seminal vesicle</option>
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106 <option value="skeletal muscle" >Skeletal muscle</option>
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107 <option value="skin 1" >Skin 1</option>
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108 <option value="skin 2" >Skin 2</option>
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109 <option value="small intestine" >Small intestine</option>
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110 <option value="smooth muscle" >Smooth muscle</option>
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111 <option value="soft tissue 1" >Soft tissue 1</option>
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112 <option value="soft tissue 2" >Soft tissue 2</option>
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113 <option value="spleen" >Spleen</option>
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114 <option value="stomach 1" >Stomach 1</option>
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115 <option value="stomach 2" >Stomach 2</option>
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116 <option value="testis" >Testis</option>
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117 <option value="thyroid gland" >Thyroid gland</option>
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118 <option value="tonsil" >Tonsil</option>
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119 <option value="urinary bladder" >Urinary bladder</option>
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120 <option value="vagina" >Vagina</option>
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121 </param>
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122 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False">
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123 <option value="High" selected="true">High</option>
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124 <option value="Medium">Medium</option>
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125 <option value="Low">Low</option>
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126 <option value="Not detected">Not detected</option>
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127 </param>
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128 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False">
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129 <option value="Enhanced" selected="true">Enhanced</option>
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130 <option value="Supported" selected="true">Supported</option>
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131 <option value="Approved">Approved</option>
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132 <option value="Uncertain">Uncertain</option>
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133 </param>
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134 </when>
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135 <when value="tumor">
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136 <param name="proteinatlas" type="select" label="Human Protein Atlas" >
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137 <!--options from_file="proteinatlas.loc" >
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138 <column name="name" index="1" />
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139 <column name="value" index="2" />
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140 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="Full Human Protein Atlas (23/10/18)" />
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141 <filter type="remove_value" meta_ref="proteinatlas" key="name" value="HPA Normal Tissue (23/10/18)" />
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142 </options-->
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143 <option value="tool-data/HPA_pathology_23-10-2018.tsv">HPA Tumor Tissue (23/10/18)</option>
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144 </param>
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145 <param name="cancer_tissue" type="select" label="Keep and annotate genes present in the following tissue(s)" multiple="True" display="checkboxes" optional="False">
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146 <option value="breast cancer" >Breast cancer</option>
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147 <option value="carcinoid" >Carcinoid</option>
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148 <option value="cervical cancer" >Cervical cancer</option>
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149 <option value="colorectal cancer" >Colorectal cancer</option>
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150 <option value="endometrial cancer" >Endometrial cancer</option>
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151 <option value="glioma" >Glioma</option>
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152 <option value="head and neck cancer" >Head and neck cancer</option>
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153 <option value="liver cancer" >Liver cancer</option>
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154 <option value="lung cancer" >Lung cancer</option>
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155 <option value="lymphoma" >Lymphoma</option>
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156 <option value="melanoma" >Melanoma</option>
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157 <option value="ovarian cancer" >Ovarian cancer</option>
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158 <option value="pancreatic cancer" >Pancreatic cancer</option>
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159 <option value="prostate cancer" >Prostate cancer</option>
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160 <option value="renal cancer" >Renal cancer</option>
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161 <option value="skin cancer" >Skin cancer</option>
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162 <option value="stomach cancer" >Stomach cancer</option>
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163 <option value="testis cancer" >Testis cancer</option>
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164 <option value="thyroid cancer" >Thyroid cancer</option>
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165 <option value="urothelial cancer" >Urothelial cancer</option>
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166 </param>
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167 </when>
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168 </conditional>
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169 <param name="not_mapped" type="boolean" truevalue="true" falsevalue="false" label="Would you like to include in output the IDs that do not match criteria or not mapped in HPA?" checked="true"/>
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170 </inputs>
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171 <outputs>
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172 <data name="hpa_output" format="tsv" label="" />
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173 </outputs>
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174 <tests>
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175 <test>
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176 <conditional name="input">
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177 <param name="ids" value="file"/>
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178 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/>
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179 <param name="header" value="true"/>
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180 <param name="ncol" value="c8"/>
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181 </conditional>
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182 <conditional name="options">
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183 <param name="database" value="normal"/>
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184 <param name="proteinatlas" value="normal_tissue.tsv"/>
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185 <param name="normal_tissue" value="bronchus,lung,nasopharynx,salivary gland"/>
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186 <param name="level" value="Not detected,Medium,High,Low"/>
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187 <param name="reliability" value="Approved,Supported,Uncertain"/>
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188 </conditional>
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189 <param name="not_mapped" value="true" />
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190 <output name="hpa_output" file="Expres_levels_Lacombe_et_al_2017_OK.txt"/>
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191 </test>
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192 </tests>
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193 <help><![CDATA[
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194 This tool retrieve information from Human Protein Atlas (https://www.proteinatlas.org/)
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195 regarding the expression profiles of human genes both on the mRNA and protein level.
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196
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197 A list of ENSG (Ensembl gene) IDs must be entered (either via a copy/paste or by choosing a file),
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198 if it's not the case, please use the ID_Convert tool from ProteoRE.
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199
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200 The resources from Human Protein Atlas that can be queried are the following:
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201
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202 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays.
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203
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204 The tab-separated file includes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell type"), expression value ("Level"), and the gene reliability of the expression value ("Reliability").
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205
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206 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
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207
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208 * **Human tumor tissue data**: staining profiles for proteins in human tumor tissue based on immunohistochemisty using tissue micro arrays and log-rank P value for Kaplan-Meier analysis of correlation between mRNA expression level and patient survival.
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209
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210 The tab-separated file includes Ensembl gene identifier ("Gene"), gene name ("Gene name"), tumor name ("Cancer"), the number of patients annotated for different staining levels ("High", "Medium", "Low" & "Not detected") and log-rank p values for patient survival and mRNA correlation ("prognostic - favourable", "unprognostic - favourable", "prognostic - unfavourable", "unprognostic - unfavourable").
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211
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212 The data is based on The Human Protein Atlas version 18 and Ensembl version 88.38.
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213
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214 -----
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215
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216 **Reliability score**
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217
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218 Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect
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219 to the definitions from HPA:
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220
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221 Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene
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222 have obtained enhanced validation based on orthogonal or independent antibody validation method.
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223
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224 Supported - Consistency with RNA-seq and/or protein/gene characterization data,
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225 in combination with similar staining pattern if independent antibodies are available.
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226
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227 Approved - Consistency with RNA-seq data in combination with inconsistency with, or lack of,
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228 protein/gene characterization data. Alternatively, consistency with protein/gene characterization data
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229 in combination with inconsistency with RNA-seq data. If independent antibodies are available,
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230 the staining pattern is partly similar or dissimilar.
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231
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232 Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data,
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233 in combination with dissimilar staining pattern if independent antibodies are available.
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234
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235 -----
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236
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237 .. class:: infomark
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238
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239 **Authors**
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240
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241 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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242
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243 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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244
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245 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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246
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247 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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248
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249 ]]></help>
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250 <citations>
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251 </citations>
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252 </tool>