Mercurial > repos > proteore > proteore_pathview_mapping

annotate Pathview.xml @ 8:33c9bd75882a draft

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planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
author proteore
date Thu, 30 Aug 2018 06:12:51 -0400
parents b617d4bbebf8
children 560541195c3f
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1 <tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.30">
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2 <requirements>
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3 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 Rscript $__tool_directory__/PathView.R
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7 #if $input.ids == "text"
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8 --id_list="$input.txt"
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9 #else
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10 --input="$input.file"
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11 --id_column="$input.ncol"
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12 --header="$input.header"
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13 #end if
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14 #if $species.pathways.pathways_id != "pathways_file"
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15 --pathways_id="$species.pathways.pids"
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16 #else
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17 --pathways_input="$species.pathways.file"
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18 --header2="$species.pathways.header2"
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19 --pathway_col="$species.pathways.ncol2"
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20 #end if
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21 --id_type="$id_type"
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22 --native_kegg="$native"
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23
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24 #if $input.ids=="file"
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25 #if $input.expression_values.nb_exp =="1"
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26 --expression_values1="$input.expression_values.e1"
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27 #else if $input.expression_values.nb_exp =="2"
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28 --expression_values1="$input.expression_values.e1"
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29 --expression_values2="$input.expression_values.e2"
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30 #else if $input.expression_values.nb_exp =="3"
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31 --expression_values1="$input.expression_values.e1"
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32 --expression_values2="$input.expression_values.e2"
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33 --expression_values3="$input.expression_values.e3"
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34 #end if
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35 #end if
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36
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37 --species=${species.ref_file}
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38
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39 ]]></command>
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40 <inputs>
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41 <param name="id_type" type="select" label="Select your identifiers type :">
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42 <option value="uniprotID">Uniprot Accession number</option>
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43 <option value="geneID">Entrez gene ID</option>
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44 </param>
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45 <conditional name="input" >
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46 <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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47 <option value="text">Copy/paste your identifiers</option>
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48 <option value="file" selected="true">Input file containing your identifiers</option>
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49 </param>
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50 <when value="text" >
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51 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
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52 <sanitizer invalid_char=''>
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53 <valid initial="string.printable">
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54 <remove value="&apos;"/>
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55 </valid>
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56 <mapping initial="none">
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57 <add source="&apos;" target="__sq__"/>
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58 </mapping>
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59 </sanitizer>
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60 </param>
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61 </when>
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62 <when value="file" >
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63 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
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64 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
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65 <param name="ncol" type="text" value="c1" label="The column which contains your 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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66 <conditional name="expression_values">
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67 <param name="nb_exp" type="select" label="How many expression values column in your file ?">
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68 <option value="0" >0</option>
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69 <option value="1" >1</option>
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70 <option value="2" >2</option>
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71 <option value="3" >3</option>
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72 </param>
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73 <when value="0">
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74 </when>
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75 <when value="1">
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76 <param name="e1" type="text" value="" label="First column number of your expression data" 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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77 </when>
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78 <when value="2">
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79 <param name="e1" type="text" value="" label="First column number of your expression data"/>
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80 <param name="e2" type="text" value="" label="Second column number of your expression data"/>
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81 </when>
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82 <when value="3">
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83 <param name="e1" type="text" value="" label="First column number of your expression data"/>
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84 <param name="e2" type="text" value="" label="Second column number of your expression data"/>
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85 <param name="e3" type="text" value="" label="Third column number of your expression data"/>
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86 </when>
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87 </conditional>
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88 </when>
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89 </conditional>
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90 <conditional name="species">
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91 <param name="ref_file" type="select" label="Select species" >
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92 <option value="hsa">Human (hsa)</option>
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93 <option value="mmu">Mouse (mmu)</option>
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94 </param>
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95 <when value="hsa">
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96 <conditional name="pathways">
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97 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
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98 <option value="pathways_names">KEGG pathway name(s)</option>
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99 <option value="pathways_ids">KEGG pathway id(s)</option>
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100 <option value="pathways_file">KEGG pathway id(s) from file</option>
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101 </param>
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102 <when value="pathways_names">
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103 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
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104 <options from_data_table="hsa_pathways">
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105 <filter type="sort_by" column="1"/>
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106 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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107 </options>
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108 </param>
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109 </when>
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110 <when value="pathways_ids">
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111 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412" or "path:hsa00010"'>
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112 <sanitizer invalid_char=''>
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113 <valid initial="string.printable">
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114 <remove value="&apos;"/>
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115 </valid>
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116 <mapping>
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117 <add source="&#x20;" target=""/>
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118 </mapping>
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119 </sanitizer>
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120 </param>
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121 </when>
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122 <when value="pathways_file">
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123 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
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124 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
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125 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways 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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126 </when>
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127 </conditional>
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128 </when>
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129 <when value="mmu">
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130 <conditional name="pathways">
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131 <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
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132 <option value="pathways_names">KEGG pathway name(s)</option>
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133 <option value="pathways_ids">KEGG pathway id(s)</option>
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134 <option value="pathways_file">KEGG pathway id(s) from file</option>
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135 </param>
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136 <when value="pathways_names">
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137 <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'>
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138 <options from_data_table="mmu_pathways">
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139 <filter type="sort_by" column="1"/>
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140 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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141 </options>
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142 </param>
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143 </when>
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144 <when value="pathways_ids">
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145 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "path:mmu00053" or "mmu00053,mmu00340" or "00053"'>
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146 <sanitizer invalid_char=''>
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147 <valid initial="string.printable">
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148 <remove value="&apos;"/>
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149 </valid>
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150 <mapping>
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151 <add source="&#x20;" target=""/>
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152 </mapping>
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153 </sanitizer>
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154 </param>
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155 </when>
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156 <when value="pathways_file">
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157 <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id " help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
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158 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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159 <param name="ncol2" type="text" value="c1" label="The column which contains your pathways 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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160 </when>
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161 </conditional>
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162 </when>
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163 </conditional>
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164 <param name="native" type="select" label="Choose the output graph format">
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165 <option value="true">KEGG graph (.png)</option>
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166 <option value="false">Graphviz layout engine (.pdf)</option>
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167 </param>
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168 </inputs>
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169 <outputs>
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170 <data name="graphviz_from_file" format="pdf" label="KEGG mapping with ${input.file.name}">
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171 <filter>native=="false" and input["ids"] == "file"</filter>
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172 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
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173 </data>
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174 <data name="kegg_from_file" format="png" label="KEGG mapping with ${input.file.name}">
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175 <filter>native=="true" and input["ids"] == "file"</filter>
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176 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/>
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177 </data>
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178 <data name="graphviz_from_list" format="pdf" label="KEGG mapping with given ids">
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179 <filter>native=="false" and input["ids"] == "text"</filter>
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180 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
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181 </data>
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182 <data name="kegg_from_list" format="png" label="KEGG mapping with given ids">
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183 <filter>native=="true" and input["ids"] == "text"</filter>
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184 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pathview.*\.png" ext="png" visible="true" assign_primary_output="true"/>
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185 </data>
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186 </outputs>
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187 <tests>
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188 <test>
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189 <conditional name="input">
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190 <param name="ids" value="file"/>
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191 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
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192 <param name="header" value="true"/>
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193 <param name="ncol" value="c1"/>
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194 </conditional>
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195 <conditional name="pathways">
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196 <param name="pathways_id" value="pathways_ids"/>
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197 <param name="pids" value="04514,05167,00010"/>
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198 </conditional>
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199 <param name="id_type" value="uniprotID"/>
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200 <param name="species" value="hsa"/>
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201 <param name="native" value="true"/>
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202 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
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203 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
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204 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
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205 </test>
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206 </tests>
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207 <help><![CDATA[
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208 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
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209
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210 Select your identifier type : UniprotAC or Entrez gene ID
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211
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212 Select an input file containing ids in a column, set header and column number or copy/paste your ids.
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213
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214 You can import 1 to 3 column(s) of expression values if you are importing ids from a file.
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215
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216 Select a species of interest.
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217
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218 Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file.
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219
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220 Select the graph format : KEGG (jpg) or graphviz (pdf)
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221
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222 Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.
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223
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224 Output : One file (png or pdf) for each selected pathway.
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225
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226 -----
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227
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228 .. class:: infomark
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229
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230 **Authors**
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231
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232 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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233
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234 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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235
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236 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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237
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238 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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239 ]]></help>
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240 <citations>
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241 <citation type="doi">10.1093/nar/gkx372</citation>
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242 <citation type="bibtex">
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243 @misc{renameTODO,
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244 author = {Weijun Luo},
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245 year = {2013},
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246 title = {pathview},
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247 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
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248 }</citation>
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249 </citations>
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250 </tool>