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1 <tool id="biofilter" name="Sort your proteins by tissue expression profiles (From HPA)" version="0.1.0">
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2 <description>selects/discards proteins according to their expression profiles (absence/presence) in a list of tissues/organs)
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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><![CDATA[
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10 python $__tool_directory__/sort_by_tissue.py
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11 --input
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12 #if $input.ids == "text"
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13 "$input.txt" "list"
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14 #else if $input.ids == "file"
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15 "$input.file" "file" "$input.header" "$input.ncol"
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16 #end if
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17 --hpa "$__tool_directory__/normal_tissue.csv"
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18 -o "$hpa_output"
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19 --tissues_del "$opt_del.tdel"
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20 --trash "$trash_output"
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21 --trash_file_detail "$trash_detail_output"
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22 --na_file "$na_file"
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23 #if $opt_keep.tkeep:
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24 --tissues_keep "$opt_keep.tkeep"
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <conditional name="input" >
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29 <param name="ids" type="select" label="Please provide your ENSG identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
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30 <option value="text">Copy/paste your identifiers</option>
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31 <option value="file">Input file containing your identifiers</option>
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32 </param>
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33 <when value="text" >
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34 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
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35 <sanitizer>
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36 <valid initial="string.printable">
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37 <remove value="'"/>
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38 </valid>
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39 <mapping initial="none">
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40 <add source="'" target="__sq__"/>
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41 </mapping>
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42 </sanitizer>
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43 </param>
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44 </when>
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45 <when value="file" >
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46 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
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47 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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48 <param name="ncol" type="text" label="The column number of ENSG 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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49 </when>
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50 </conditional>
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51 <section name="opt_del" title="Step 1: Eliminate from my list genes expressed in the following tissue(s)" expanded="True">
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52 <param name="tdel" type="select" label="Eliminate from my list genes expressed in the following tissue(s)" multiple="True" display="checkboxes">
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53 <option value="adrenal gland" >Adrenal gland</option>
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54 <option value="appendix" >Appendix</option>
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55 <option value="bone marrow" >Bone marrow</option>
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56 <option value="breast" >Breast</option>
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57 <option value="bronchus" >Bronchus</option>
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58 <option value="caudate" >Caudate</option>
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59 <option value="cerebellum" >Cerebellum</option>
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60 <option value="cerebral cortex" >Cerebral cortex</option>
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61 <option value="cervix" >Cervix</option>
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62 <option value="colon" >Colon</option>
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63 <option value="duodenum" >Duodenum</option>
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64 <option value="endometrium 1" >Endometrium 1</option>
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65 <option value="endometrium 2" >Endometrium 2</option>
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66 <option value="epididymis" >Epididymis</option>
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67 <option value="esophagus" >Esophagus</option>
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68
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69 <option value="fallopian tube" >Fallopian tube</option>
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70 <option value="gallbladder" >Gallbladder</option>
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71
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72 <option value="heart muscle" >Heart muscle</option>
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73 <option value="hippocampus" >Hippocampus</option>
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74
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75 <option value="kidney" >Kidney</option>
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76
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77 <option value="liver" >Liver</option>
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78 <option value="lung" >Lung</option>
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79 <option value="lymph node" >Lymph node</option>
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80 <option value="nasopharynx" >Nasopharynx</option>
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81 <option value="oral mucosa" >Oral mucosa</option>
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82 <option value="ovary" >Ovary</option>
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83 <option value="pancreas" >Pancreas</option>
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84 <option value="parathyroid gland" >Parathyroid gland</option>
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85
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86 <option value="placenta" >Placenta</option>
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87 <option value="prostate" >Prostate</option>
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88 <option value="rectum" >Rectum</option>
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89
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90 <option value="salivary gland" >Salivary gland</option>
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91 <option value="seminal vesicle" >Seminal vesicle</option>
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92 <option value="skeletal muscle" >Skeletal muscle</option>
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93 <option value="skin 1" >Skin 1</option>
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94 <option value="skin 2" >Skin 2</option>
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95
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96 <option value="small intestine" >Small intestine</option>
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97 <option value="smooth muscle" >Smooth muscle</option>
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98 <option value="soft tissue 1" >Soft tissue 1</option>
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99 <option value="soft tissue 2" >Soft tissue 2</option>
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100 <option value="spleen" >Spleen</option>
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101 <option value="stomach 1" >Stomach 1</option>
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102 <option value="stomach 2" >Stomach 2</option>
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103 <option value="testis" >Testis</option>
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104 <option value="thyroid gland" >Thyroid gland</option>
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105 <option value="tonsil" >Tonsil</option>
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106 <option value="urinary bladder" >Urinary bladder</option>
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107 <option value="vagina" >Vagina</option>
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108 </param>
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109 </section>
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110 <section name="opt_keep" title="Step 2 (optional): Choose tissues where expressed genes need to be kept even if expressed in list of tissues in step 1" expanded="False">
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111 <param name="tkeep" type="select" label="Choose tissues where expressed genes need to be kept even if expressed in list of tissues in step 1" multiple="True" optional="True" display="checkboxes" >
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112 <option value="adrenal gland" >Adrenal gland</option>
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113 <option value="appendix" >Appendix</option>
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114 <option value="bone marrow" >Bone marrow</option>
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115 <option value="breast" >Breast</option>
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116 <option value="bronchus" >Bronchus</option>
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117 <option value="caudate" >Caudate</option>
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118 <option value="cerebellum" >Cerebellum</option>
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119 <option value="cerebral cortex" >Cerebral cortex</option>
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120 <option value="cervix" >Cervix</option>
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121 <option value="colon" >Colon</option>
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122 <option value="duodenum" >Duodenum</option>
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123 <option value="endometrium 1" >Endometrium 1</option>
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124 <option value="endometrium 2" >Endometrium 2</option>
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125 <option value="epididymis" >Epididymis</option>
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126 <option value="esophagus" >Esophagus</option>
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127
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128 <option value="fallopian tube" >Fallopian tube</option>
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129 <option value="gallbladder" >Gallbladder</option>
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130
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131 <option value="heart muscle" >Heart muscle</option>
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132 <option value="hippocampus" >Hippocampus</option>
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133
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134 <option value="kidney" >Kidney</option>
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135
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136 <option value="liver" >Liver</option>
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137 <option value="lung" >Lung</option>
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138 <option value="lymph node" >Lymph node</option>
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139 <option value="nasopharynx" >Nasopharynx</option>
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140 <option value="oral mucosa" >Oral mucosa</option>
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141 <option value="ovary" >Ovary</option>
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142 <option value="pancreas" >Pancreas</option>
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143 <option value="parathyroid gland" >Parathyroid gland</option>
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144
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145 <option value="placenta" >Placenta</option>
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146 <option value="prostate" >Prostate</option>
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147 <option value="rectum" >Rectum</option>
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148
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149 <option value="salivary gland" >Salivary gland</option>
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150 <option value="seminal vesicle" >Seminal vesicle</option>
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151 <option value="skeletal muscle" >Skeletal muscle</option>
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152 <option value="skin 1" >Skin 1</option>
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153 <option value="skin 2" >Skin 2</option>
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154
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155 <option value="small intestine" >Small intestine</option>
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156 <option value="smooth muscle" >Smooth muscle</option>
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157 <option value="soft tissue 1" >Soft tissue 1</option>
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158 <option value="soft tissue 2" >Soft tissue 2</option>
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159 <option value="spleen" >Spleen</option>
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160 <option value="stomach 1" >Stomach 1</option>
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161 <option value="stomach 2" >Stomach 2</option>
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162 <option value="testis" >Testis</option>
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163 <option value="thyroid gland" >Thyroid gland</option>
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164 <option value="tonsil" >Tonsil</option>
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165 <option value="urinary bladder" >Urinary bladder</option>
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166 <option value="vagina" >Vagina</option>
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167 </param>
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168 </section>
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169 </inputs>
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170 <outputs>
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171 <data name="hpa_output" format="tabular" label="HPA selection" />
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172 <data name="trash_detail_output" format="tabular" label="HPA information of excluded genes" />
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173 <data name="trash_output" format="tabular" label="Excluded genes ID" />
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174 <data name="na_file" format="tabular" label="Genes without tissues information" />
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175 </outputs>
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176 <tests>
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177 <test>
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178 <conditional name="input">
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179 <param name="ids" value="file" />
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180 <param name="file" value="IDs.txt" />
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181 <param name="header" value="true" />
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182 <param name="ncol" value="c3" />
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183 </conditional>
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184 <section name="opt_del">
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185 <param name="tdel" value="salivary gland" />
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186 </section>
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187 <section name="opt_keep">
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188 <param name="tkeep" value="lung" />
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189 </section>
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190 <output name="hpa_output" file="sort_by_tissue_output.txt" />
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191 <output name="trash_detail_output" file="trash_detail_sort_by_tissue.txt" />
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192 <output name="trash_output" file="trash_sort_by_tissue.txt" />
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193 <output name="na_file" file="na_sort_by_tissue.txt" />
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194 </test>
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195 </tests>
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196 <help><![CDATA[
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197 This tool filters the proteins according to their tissue(s) of origin using Human Protein Atlas (http://www.proteinatlas.org/).
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198
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199 **Input**
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200
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201 This tool requires a list of ENSG IDs, by copy/paste into text field or choose from a file.
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202
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203 **Option**
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204
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205 Firstly, you can choose tissues in which genes expressed need to be eliminated. If among these eliminated genes, you want to keep genes expressed in some other tissues, you can choose these tissues in the second list.
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206
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207 For example, when you want to eliminate from input file the genes that are expressed in salivary, but among these genes, you want to keep the genes that are also expressed in lung:
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208
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209 * Step 1: choose salivary gland
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210
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211 * Step 2: choose lung
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212
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213 -----
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214
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215 .. class:: infomark
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216
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217 **Authors**
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218
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219 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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220 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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221
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222 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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223
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224 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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225
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226 ]]></help>
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227 <citations>
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228 </citations>
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229 </tool>
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