Mercurial > repos > proteore > proteore_pathview_mapping

annotate kegg_pathways_visualization.xml @ 13:c59ec7fce7b3 draft

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author proteore
date Fri, 09 Nov 2018 05:16:58 -0500
parents 9fe4a861601b
children be8115c73b0d
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1 <tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.09">
12
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2 <description>map visualisation (PathView)</description>
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3 <requirements>
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4 <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 Rscript $__tool_directory__/kegg_pathways_visualization.R
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8 #if $input.ids == "text"
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9 --id_list="$input.txt"
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10 #else
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11 --input="$input.file"
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12 --id_column="$input.ncol"
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13 --header="$input.header"
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14 #end if
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15 #if $species.pathways.pathways_id != "pathways_file"
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16 --pathways_id="$species.pathways.pids"
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17 #else
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18 --pathways_input="$species.pathways.file"
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19 --header2="$species.pathways.header2"
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20 --pathway_col="$species.pathways.ncol2"
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21 #end if
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22 --id_type="$id_type"
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23 --native_kegg="$native"
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24
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25
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26 #if $input.ids=="file" and $input.foldchange.fc=="true"
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27 --fold_change_data="$input.foldchange.fc"
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28 --fold_change_col="$input.foldchange.fc_col"
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29 #else
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30 --fold_change_data="false"
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31 #end if
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32
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33 --species=${species.ref_file}
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34 --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] }
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35 --output="$text_output"
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36
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37 ]]></command>
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38 <inputs>
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39 <conditional name="species">
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40 <param name="ref_file" type="select" label="Select species" >
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41 <option value="hsa">Human (H. sapiens)</option>
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42 <option value="mmu">Mouse (M. musculus)</option>
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43 <option value="rno">Rat (R. norvegicus)</option>
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44 </param>
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45 <when value="hsa">
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46 <conditional name="pathways">
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47 <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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48 <option value="pathways_names">KEGG pathway name(s)</option>
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49 <option value="pathways_ids">KEGG pathway id(s)</option>
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50 <option value="pathways_file">KEGG pathway id(s) from file</option>
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51 </param>
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52 <when value="pathways_names">
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53 <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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54 <options from_data_table="hsa_pathways">
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55 <filter type="sort_by" column="1"/>
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56 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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57 </options>
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58 </param>
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59 </when>
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60 <when value="pathways_ids">
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61 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
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62 <sanitizer invalid_char=''>
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63 <valid initial="string.printable">
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64 <remove value="&apos;"/>
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65 </valid>
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66 <mapping>
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67 <add source="&#x20;" target=""/>
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68 </mapping>
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69 </sanitizer>
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70 </param>
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71 </when>
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72 <when value="pathways_file">
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73 <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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74 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
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75 <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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76 </when>
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77 </conditional>
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78 </when>
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79 <when value="mmu">
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80 <conditional name="pathways">
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81 <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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82 <option value="pathways_names">KEGG pathway name(s)</option>
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83 <option value="pathways_ids">KEGG pathway id(s)</option>
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84 <option value="pathways_file">KEGG pathway id(s) from file</option>
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85 </param>
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86 <when value="pathways_names">
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87 <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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88 <options from_data_table="mmu_pathways">
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89 <filter type="sort_by" column="1"/>
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90 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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91 </options>
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92 </param>
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93 </when>
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94 <when value="pathways_ids">
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95 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "mmu00053 mmu00340"'>
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96 <sanitizer invalid_char=''>
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97 <valid initial="string.printable">
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98 <remove value="&apos;"/>
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99 </valid>
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100 <mapping>
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101 <add source="&#x20;" target=""/>
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102 </mapping>
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103 </sanitizer>
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104 </param>
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105 </when>
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106 <when value="pathways_file">
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107 <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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108 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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109 <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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110 </when>
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111 </conditional>
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112 </when>
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113 <when value="rno">
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114 <conditional name="pathways">
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115 <param name="pathways_id" type="select" label="Enter your pathway(s) name/id" help="Enter KEGG pathway name(s) or KEGG pathway id(s)">
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116 <option value="pathways_names">KEGG pathway name(s)</option>
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117 <option value="pathways_ids">KEGG pathway id(s)</option>
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118 <option value="pathways_file">KEGG pathway id(s) from file</option>
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119 </param>
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120 <when value="pathways_names">
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121 <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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122 <options from_data_table="rno_pathways">
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123 <filter type="sort_by" column="1"/>
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124 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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125 </options>
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126 </param>
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127 </when>
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128 <when value="pathways_ids">
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129 <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by tab, space or carriage return into the form field, for example: "hsa00010 hsa05412"'>
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130 <sanitizer invalid_char=''>
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131 <valid initial="string.printable">
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132 <remove value="&apos;"/>
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133 </valid>
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134 <mapping>
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135 <add source="&#x20;" target=""/>
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136 </mapping>
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137 </sanitizer>
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138 </param>
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139 </when>
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140 <when value="pathways_file">
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141 <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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142 <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
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143 <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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144 </when>
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145 </conditional>
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146 </when>
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147 </conditional>
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148 <param name="id_type" type="select" label="Select your identifiers type :">
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149 <option value="uniprotID">Uniprot Accession number</option>
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150 <option value="geneID">Entrez gene ID</option>
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151 <!--option value="keggid">KEGG genes ID</option-->
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152 </param>
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153 <conditional name="input" >
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154 <param name="ids" type="select" label="Enter your identifiers (Uniprot AC or Entrez gene ID)" help="Copy/paste or ID list from a file (e.g. table)" >
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155 <option value="text">Copy/paste your identifiers</option>
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156 <option value="file" selected="true">Input file containing your identifiers</option>
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157 </param>
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158 <when value="text" >
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159 <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
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160 <sanitizer invalid_char=''>
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161 <valid initial="string.printable">
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162 <remove value="&apos;"/>
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163 </valid>
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164 <mapping initial="none">
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165 <add source="&apos;" target="__sq__"/>
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166 </mapping>
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167 </sanitizer>
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168 </param>
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169 </when>
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170 <when value="file" >
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171 <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
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172 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
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173 <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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174 <conditional name="foldchange" >
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175 <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Do you have fold change values to represent on the graph ?"/>
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176 <when value="true">
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177 <param name="fc_col" type="text" label="Please enter column(s) number of fold change data separated by ','. 3 columns max" help="For example : c1,c3,c4"/>
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178 </when>
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179 <when value="false"/>
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180 </conditional>
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181 </when>
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182 </conditional>
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183 <param name="native" type="select" label="Choose the output graphical format">
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184 <option value="true">KEGG map (.png)</option>
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185 <option value="false">Graphviz layout engine (.pdf)</option>
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186 </param>
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187 </inputs>
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188 <outputs>
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189 <data name="text_output" format="tsv" label="KEGG pathways visualization text output"/>
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190 <collection type="list" label="KEGG pathways map from ${input.file.name}" name="graphviz_output_from_file">
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191 <filter>native=="false" and input["ids"] == "file"</filter>
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192 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
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193 </collection>
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194 <collection type="list" label="KEGG pathways map from ${input.file.name}" name="kegg_graph_output_from_file">
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195 <filter>native=="true" and input["ids"] == "file"</filter>
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196 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png"/>
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197 </collection>
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198 <collection type="list" label="KEGG pathways map" name="graphviz_output_from_list">
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199 <filter>native=="false" and input["ids"] == "text"</filter>
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200 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.pdf" ext="pdf" />
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201 </collection>
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202 <collection type="list" label="KEGG pathways map" name="kegg_graph_output_from_list">
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203 <filter>native=="true" and input["ids"] == "text"</filter>
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204 <discover_datasets pattern="(?P&lt;designation&gt;.+\..*)\.png" ext="png" />
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205 </collection>
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206 </outputs>
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207 <tests>
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208 <!--test>
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209 <conditional name="input">
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210 <param name="ids" value="file"/>
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211 <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
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212 <param name="header" value="true"/>
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213 <param name="ncol" value="c1"/>
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214 </conditional>
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215 <conditional name="pathways">
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216 <param name="pathways_id" value="pathways_ids"/>
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217 <param name="pids" value="04514,05167,00010"/>
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218 </conditional>
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219 <param name="id_type" value="uniprotID"/>
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220 <param name="species" value="hsa"/>
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221 <param name="native" value="true"/>
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222 <output name="kegg_from_file" file="hsa04514.pathview.png" compare="sim_size"/>
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223 <output name="kegg_from_file" file="hsa05167.pathview.png" compare="sim_size"/>
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224 <output name="kegg_from_file" file="hsa00010.pathview.png" compare="sim_size"/>
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225 </test-->
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226 </tests>
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227 <help><![CDATA[
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228 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
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229
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230 You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
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231
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232 If your input have another type of IDs, please use the ID_Converter tool.
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233
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234 **Input:**
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235
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236
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237 - KEGG Pathways IDs to be used for mapping can be set by:
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238 - chosing from the KEGG pathways name list
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239 - giving a list (copy/paste)
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240 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
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241 - Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number.
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242 - fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map)
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243
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244 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
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245
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246 .. csv-table:: Simulated data
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247 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
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248
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249 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
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250 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
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251 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
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252 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
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253
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254 |
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255
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256 **Output:**
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257
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258 - a **collection dataset** named 'KEGG pathways map from <dataset>', one file (png or pdf) for each given pathway.
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259 - a **summary text file** (.tsv) of the mapping(s) with the following columns
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260 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
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261 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
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262 - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs
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263 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
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264 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
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265 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
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266 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
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267 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
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268 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
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269
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270 -----
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271
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272 .. class:: infomark
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273
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274 **Database:**
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275
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276 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
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277
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278 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html
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279
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280
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281 -----
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282
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283 .. class:: infomark
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284
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285 **Authors**
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286
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287 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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288
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289 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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290
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291 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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292
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293 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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294 ]]></help>
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295 <citations>
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296 <citation type="doi">10.1093/nar/gkx372</citation>
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297 <citation type="bibtex">
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298 @misc{renameTODO,
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299 author = {Weijun Luo},
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300 year = {2013},
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301 title = {pathview},
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302 url = {https://bioconductor.org/packages/release/bioc/html/pathview.html},
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303 }</citation>
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304 </citations>
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305 </tool>