Mercurial > repos > proteore > proteore_expression_levels_by_tissue
annotate get_expression_profiles.xml @ 9:0a0f6c37f05e draft
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author | proteore |
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date | Wed, 13 Mar 2019 09:15:52 -0400 |
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1 <tool id="sel_ann_hpa" name="Get expression profiles" version="2019.03.06"> |
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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 $__tool_directory__/get_expression_profiles.R |
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11 |
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12 #if "protein_atlas" in str($options.proteinatlas).split("/") |
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13 --ref_file="$options.proteinatlas" |
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14 #else |
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15 --ref_file="$__tool_directory__/$options.proteinatlas" |
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16 #end if |
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17 |
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18 --input_type="$input.ids" |
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19 #if $input.ids == "list" |
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20 --input="$input.list" |
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21 #else |
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22 --input="$input.file" |
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23 --column_number="$input.ncol" |
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24 --header="$input.header" |
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25 #end if |
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26 |
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27 #if $options.database == "normal" |
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28 --atlas="normal" |
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29 --tissue="$options.normal_tissue" |
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30 --level="$options.level" |
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31 --reliability="$options.reliability" |
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32 #else if $options.database == "tumor" |
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33 --atlas="cancer" |
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34 --cancer="$options.cancer_tissue" |
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35 #end if |
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36 --not_mapped="$not_mapped" |
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37 --output="$hpa_output" |
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38 </command> |
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39 <inputs> |
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40 <conditional name="input" > |
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41 <param name="ids" type="select" label="Enter your IDs (ENSG IDs only)" help="Copy/paste or from a file (e.g. table)" > |
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42 <option value="list">Copy/paste your IDs</option> |
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43 <option value="file" selected="true">Input file containing your IDs</option> |
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44 </param> |
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45 <when value="list" > |
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46 <param name="list" type="text" label="Copy/paste your IDs" help='IDs must be separated by spaces into the form field, for example: ENSG00000174876 ENSG00000178372 ENSG00000159763' > |
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47 <sanitizer> |
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48 <valid initial="string.printable"> |
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49 <remove value="'"/> |
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50 </valid> |
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51 <mapping initial="none"> |
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52 <add source="'" target="__sq__"/> |
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53 </mapping> |
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54 </sanitizer> |
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55 </param> |
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56 </when> |
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57 <when value="file" > |
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58 <param name="file" type="data" format="txt,tabular" label="" help="" /> |
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59 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> |
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60 <param name="ncol" type="text" value="c1" label="Column number of 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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61 <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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62 </param> |
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63 </when> |
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64 </conditional> |
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65 <conditional name="options"> |
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66 <param name="database" type="select" label="Human Protein Atlas (normal or tumor tissue)"> |
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67 <option value="normal">Human Normal Tissue</option> |
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68 <option value="tumor">Human Tumor Tissue</option> |
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69 </param> |
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70 <when value="normal"> |
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71 <param name="proteinatlas" type="select" label="Normal tissue HPA version" > |
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72 <options from_data_table="proteore_protein_atlas_normal_tissue"/> |
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73 </param> |
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74 <param name="normal_tissue" type="select" label="Select tissue(s)" multiple="True" display="checkboxes" optional="False"> |
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75 <option value="adrenal gland" >Adrenal gland</option> |
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76 <option value="appendix" >Appendix</option> |
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77 <option value="bone marrow" >Bone marrow</option> |
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78 <option value="breast" >Breast</option> |
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79 <option value="bronchus" >Bronchus</option> |
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80 <option value="caudate" >Caudate</option> |
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81 <option value="cerebellum" >Cerebellum</option> |
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82 <option value="cerebral cortex" >Cerebral cortex</option> |
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83 <option value="cervix" >Cervix</option> |
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84 <option value="colon" >Colon</option> |
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85 <option value="duodenum" >Duodenum</option> |
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86 <option value="endometrium 1" >Endometrium 1</option> |
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87 <option value="endometrium 2" >Endometrium 2</option> |
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88 <option value="epididymis" >Epididymis</option> |
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89 <option value="esophagus" >Esophagus</option> |
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90 <option value="fallopian tube" >Fallopian tube</option> |
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91 <option value="gallbladder" >Gallbladder</option> |
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92 <option value="heart muscle" >Heart muscle</option> |
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93 <option value="hippocampus" >Hippocampus</option> |
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94 <option value="kidney" >Kidney</option> |
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95 <option value="liver" >Liver</option> |
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96 <option value="lung" >Lung</option> |
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97 <option value="lymph node" >Lymph node</option> |
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98 <option value="nasopharynx" >Nasopharynx</option> |
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99 <option value="oral mucosa" >Oral mucosa</option> |
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100 <option value="ovary" >Ovary</option> |
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101 <option value="pancreas" >Pancreas</option> |
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102 <option value="parathyroid gland" >Parathyroid gland</option> |
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103 <option value="placenta" >Placenta</option> |
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104 <option value="prostate" >Prostate</option> |
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105 <option value="rectum" >Rectum</option> |
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106 <option value="salivary gland" >Salivary gland</option> |
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107 <option value="seminal vesicle" >Seminal vesicle</option> |
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108 <option value="skeletal muscle" >Skeletal muscle</option> |
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109 <option value="skin 1" >Skin 1</option> |
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110 <option value="skin 2" >Skin 2</option> |
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111 <option value="small intestine" >Small intestine</option> |
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112 <option value="smooth muscle" >Smooth muscle</option> |
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113 <option value="soft tissue 1" >Soft tissue 1</option> |
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114 <option value="soft tissue 2" >Soft tissue 2</option> |
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115 <option value="spleen" >Spleen</option> |
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116 <option value="stomach 1" >Stomach 1</option> |
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117 <option value="stomach 2" >Stomach 2</option> |
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118 <option value="testis" >Testis</option> |
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119 <option value="thyroid gland" >Thyroid gland</option> |
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120 <option value="tonsil" >Tonsil</option> |
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121 <option value="urinary bladder" >Urinary bladder</option> |
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122 <option value="vagina" >Vagina</option> |
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123 </param> |
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124 <param name="level" type="select" label="Expression level" display="checkboxes" multiple="True" optional="False"> |
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125 <option value="High" selected="true">High</option> |
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126 <option value="Medium">Medium</option> |
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127 <option value="Low">Low</option> |
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128 <option value="Not detected">Not detected</option> |
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129 </param> |
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130 <param name="reliability" type="select" label="Reliability score" display="checkboxes" multiple="True" optional="False"> |
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131 <option value="Enhanced" selected="true">Enhanced</option> |
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132 <option value="Supported" selected="true">Supported</option> |
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133 <option value="Approved">Approved</option> |
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134 <option value="Uncertain">Uncertain</option> |
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135 </param> |
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136 </when> |
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137 <when value="tumor"> |
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138 <param name="proteinatlas" type="select" label="Tumor tissue HPA version" > |
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139 <options from_data_table="proteore_protein_atlas_tumor_tissue"/> |
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140 </param> |
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141 <param name="cancer_tissue" type="select" label="Select cancer tissue(s)" multiple="True" display="checkboxes" optional="False"> |
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142 <option value="breast cancer" >Breast cancer</option> |
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143 <option value="carcinoid" >Carcinoid</option> |
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144 <option value="cervical cancer" >Cervical cancer</option> |
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145 <option value="colorectal cancer" >Colorectal cancer</option> |
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146 <option value="endometrial cancer" >Endometrial cancer</option> |
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147 <option value="glioma" >Glioma</option> |
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148 <option value="head and neck cancer" >Head and neck cancer</option> |
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149 <option value="liver cancer" >Liver cancer</option> |
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150 <option value="lung cancer" >Lung cancer</option> |
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151 <option value="lymphoma" >Lymphoma</option> |
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152 <option value="melanoma" >Melanoma</option> |
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153 <option value="ovarian cancer" >Ovarian cancer</option> |
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154 <option value="pancreatic cancer" >Pancreatic cancer</option> |
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155 <option value="prostate cancer" >Prostate cancer</option> |
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156 <option value="renal cancer" >Renal cancer</option> |
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157 <option value="skin cancer" >Skin cancer</option> |
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158 <option value="stomach cancer" >Stomach cancer</option> |
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159 <option value="testis cancer" >Testis cancer</option> |
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160 <option value="thyroid cancer" >Thyroid cancer</option> |
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161 <option value="urothelial cancer" >Urothelial cancer</option> |
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162 </param> |
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163 </when> |
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164 </conditional> |
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165 <param name="not_mapped" type="boolean" truevalue="true" falsevalue="false" label="Keep IDs not found in HPA?" checked="true"/> |
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166 </inputs> |
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167 <outputs> |
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168 <data name="hpa_output" format="tsv" label="" /> |
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169 </outputs> |
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170 <tests> |
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171 <test> |
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172 <conditional name="input"> |
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173 <param name="ids" value="file"/> |
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174 <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt"/> |
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175 <param name="header" value="true"/> |
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176 <param name="ncol" value="c8"/> |
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177 </conditional> |
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178 <conditional name="options"> |
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179 <param name="database" value="normal"/> |
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180 <param name="proteinatlas" value="normal_tissue.tsv"/> |
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181 <param name="normal_tissue" value="bronchus,lung,nasopharynx,salivary gland"/> |
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182 <param name="level" value="Not detected,Medium,High,Low"/> |
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183 <param name="reliability" value="Approved,Supported,Uncertain"/> |
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184 </conditional> |
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185 <param name="not_mapped" value="true" /> |
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186 <output name="hpa_output" file="Expres_levels_Lacombe_et_al_2017_OK.txt"/> |
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187 </test> |
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188 </tests> |
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189 <help><![CDATA[ |
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190 |
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191 **Description** |
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192 |
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193 This tool allows to retrieve expression profiles (normal or tumor tissue) from Human Protein Atlas (https://www.proteinatlas.org/) |
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194 |
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195 **Input** |
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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); if it's not the case, please use the ID_Converter tool of ProteoRE. |
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198 |
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199 ----- |
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200 |
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201 **Parameters** |
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202 |
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203 "Human Protein Atlas (normal or tumor tissue)": two resources are currently available |
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204 |
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205 * **Human normal tissue data**: expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. |
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206 |
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207 **Output** will be in the form: a 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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208 |
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209 * **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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210 |
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211 **Ouptut** will be in the form: 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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212 |
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213 "Select tissue(s)": information from more than one tissue can be retrieved |
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214 |
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215 "Keep IDs not found in HPA?": ENSG ID not found in Human Protein Atlas will be returned in the output file in the form of "NA" (default is "No") |
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216 |
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217 ----- |
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218 |
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219 **Reliability score (only for normal tissue)** |
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220 |
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221 Reliability score is divided into Enhanced, Supported, Approved, or Uncertain with respect to the definitions from HPA: |
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222 |
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223 Enhanced - One or several antibodies with non-overlapping epitopes targeting the same gene have obtained enhanced validation based on orthogonal or independent antibody validation method. |
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224 |
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225 Supported - Consistency with RNA-seq and/or protein/gene characterization data, 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, protein/gene characterization data. Alternatively, consistency with protein/gene characterization data in combination with inconsistency with RNA-seq data. If independent antibodies are available, the staining pattern is partly similar or dissimilar. |
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228 |
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229 Uncertain - Inconsistency with, or lack of, RNA-seq and/or protein/gene characterization data, in combination with dissimilar staining pattern if independent antibodies are available. |
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230 |
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231 ----- |
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232 |
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233 **Data sources (release date)** |
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234 |
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235 Both normal and tumor tissues data are based on the Human Protein Atlas version 18 and Ensembl version 88.38. |
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236 |
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237 ----- |
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238 |
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239 .. class:: infomark |
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240 |
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241 **Authors** |
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242 |
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243 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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244 |
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245 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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246 |
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247 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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248 |
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249 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. |
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250 |
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251 ]]></help> |
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252 <citations> |
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253 </citations> |
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254 </tool> |