annotate pathwaymatcher.xml @ 1:5d0c44bc354d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 7e04827e48352f6b28cf2e2c93a89a270e5bf026
author galaxyp
date Wed, 04 Jul 2018 04:28:07 -0400
parents f66af2b04a98
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1 <tool id="reactome_pathwaymatcher" name="Pathway Matcher" version="@PATHWAYMATCHER_VERSION@.@TOOL_SUBVERSION@">
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2 <description>
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3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
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4 </description>
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5 <macros>
1
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6 <token name="@PATHWAYMATCHER_VERSION@">1.8.1</token>
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7 <token name="@TOOL_SUBVERSION@">0</token>
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8 <xml name="input_fasta">
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9 <param format="fasta" name="input_database" type="data" label="Protein Database"
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10 help="Select FASTA database from history"/>
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11 </xml>
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12 </macros>
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13 <requirements>
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14 <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement>
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15 <requirement type="package" version="3.0">zip</requirement>
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16 </requirements>
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17 <stdio>
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18 <exit_code range="1:" level="fatal" description="Job Failed" />
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19 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
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20 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
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21 </stdio>
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22 <command>
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23 <![CDATA[
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24 #from datetime import datetime
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25 #import json
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26 #import os
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27 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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28 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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29 #set $temp_stderr = "pathwaym_stderr"
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30 #set $bin_dir = "bin"
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31
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32 mkdir output;
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33 cwd=`pwd`;
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34 export HOME=\$cwd;
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35
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36 #####################
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37 ## Pathway Matcher ##
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38 #####################
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39 (pathwaymatcher src.main.java.no.uib.pap.pathwaymatcher.PathwayMatcher
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40
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41 #for $i, $s in enumerate($input_types)
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42
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43 ## GENETIC VARIANTS
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44
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45 #if $s.input_type.input_type_selector == "rsid"
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46 -t rsid -i '${s.input_type.input_rsid}'
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47 #end if
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48
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49 #if $s.input_type.input_type_selector == "chrbp"
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50 -t chrbp -i '${s.input_type.input_chrbp}'
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51 #end if
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52
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53 #if $s.input_type.input_type_selector == "vcf"
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54 -t vcf -i '${s.input_type.input_vcf}'
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55 #end if
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56
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57 ## GENES
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58
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59 #if $s.input_type.input_type_selector == "gene"
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60 -t gene -i '${s.input_type.input_gene}'
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61 #end if
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62
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63 ## PEPTIDES
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64
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65 #if $s.input_type.input_type_selector == "peptide"
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66 -t peptide -i '${s.input_type.input_peptide}'
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67 -f '${s.input_type.input_database}'
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68 -r '${s.input_type.ptm_range}'
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69 #end if
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70
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71 #if $s.input_type.input_type_selector == "modifiedpeptide"
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72 -t modifiedpeptide -i '${s.input_type.input_modifiedpeptide}'
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73 -f '${s.input_type.input_database}'
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74 -r '${s.input_type.ptm_range}'
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75 #end if
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76
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77 ## PROTEINS
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78
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79 #if $s.input_type.input_type_selector == "uniprot"
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80 -t uniprot -i '${s.input_type.input_uniprot}'
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81 #end if
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82
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83 #if $s.input_type.input_type_selector == "ensembl"
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84 -t ensembl -i '${s.input_type.input_ensembl}'
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85 #end if
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86
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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87 ## PROTEOFORMS
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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88
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89 #if $s.input_type.input_type_selector == "proteoforms"
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90 #if $s.input_type.proteoform_match_criteria:
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91 -t proteoform -m '${s.input_type.proteoform_match_criteria}' -i '${s.input_type.input_proteoforms}'
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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92 #else:
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93 -t proteoform -i '${s.input_type.input_proteoforms}'
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94 #end if
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95 #end if
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96
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97 #end for
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98
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99 ## OUTPUT OPTIONS
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100
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101 #if $output_options.search_top_level_info:
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102 -tlp
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103 #end if
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104
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105 #set $output_graphs_list = str($output_options.output_graphs).split(',')
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106
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107 #if 'gg' in $output_graphs_list:
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108 -gg
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109 #end if
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110
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111 #if 'gu' in $output_graphs_list:
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112 -gu
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113 #end if
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114
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115 #if 'gp' in $output_graphs_list:
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116 -gp
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117 #end if
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118
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119 2>> $temp_stderr);
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120
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121 ## We create a folder to contain graphs files.
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122 #if $output_options.output_graphs:
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123 mkdir "graphs";
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124 #end if
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125
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126 #if 'gg' in $output_graphs_list:
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127 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
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128 #end if
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129
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130 #if 'gu' in $output_graphs_list:
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131 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
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132 #end if
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133
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134 #if 'gp' in $output_graphs_list:
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135 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
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136 #end if
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137
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138 exit_code_for_galaxy=\$?;
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139 cat $temp_stderr 2>&1;
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140 (exit \$exit_code_for_galaxy)
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141 ]]>
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142 </command>
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143 <inputs>
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144
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145 <repeat name="input_types" title="Input" min="1">
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146 <conditional name="input_type">
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147 <param name="input_type_selector" type="select" label="Input type"
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148 help="">
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149 <option value="rsid">Genetic variants - SNP rsId list</option>
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150 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
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151 <option value="vcf">Genetic variants - Variant Call Format Specification</option>
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152 <option value="gene">Genes</option>
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153 <option value="peptide">Peptides - Simple list</option>
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154 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
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155 <option value="uniprot">Proteins - UniProt Accession list</option>
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156 <option value="ensembl">Proteins - Ensembl identifier list</option>
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157 <option value="proteoforms">Proteoforms</option>
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158 </param>
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159
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160 <!-- Genetic variants -->
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161 <when value="rsid">
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162 <param format="txt" name="input_rsid" type="data" label="SNP rsId list"
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163 help="The file contains one rsid identifier as defined in dbSNP[1] on each row.
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164 The list must be ordered by chromosome and base pair (bp). The list must not have duplicates.
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165 All rsids must appear in the human assembly GRCh37.p13. "/>
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166 </when>
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167
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168 <when value="chrbp">
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169 <param format="txt" name="input_chrbp" type="data" label="Chromosomes and base pairs"
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170 help="Genetic variants can also be represented using the chromosome and the base pair numbers.
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171 The input should be sorted by chromosome number and then by base pair. "/>
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172 </when>
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173
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174 <when value="vcf">
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175 <param format="vcf" name="input_vcf" type="data" label="Variant Call Format Specification"
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176 help="The input follows the Variant Call Format Specification[2] v4.3.
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177 It also allows the possibility to specify only the first 4 columns in the data section of the file:
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178 CHROM, POS, ID, REF. "/>
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179 </when>
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180
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181 <!-- Genes -->
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182 <when value="gene">
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183 <param format="txt" name="input_gene" type="data" label="Genes"
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184 help="File with a one gene name in each line. Genes follow the HUGO gene nomenclature[3]."/>
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185 </when>
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186
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187 <!-- Peptides -->
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188 <when value="peptide">
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189 <param format="txt" name="input_peptide" type="data" label="Simple list"
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190 help="File with a one peptide sequence in each line."/>
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191
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192 <expand macro="input_fasta" />
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193
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194 <param name="ptm_range" type="integer" value="0" label="PTM position range" optional="true"
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195 help="Plus minus positions for the same PTM site."/>
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196 </when>
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197
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198 <when value="modifiedpeptide">
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199 <param format="txt" name="input_modifiedpeptide" type="data" label="Peptide List with PTM types and sites"
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200 help="Each line of the file corresponds to a single peptide with post-translational modifications."/>
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201
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202 <expand macro="input_fasta" />
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203
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204 <param name="ptm_range" type="integer" value="0" label="PTM position range" optional="true"
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205 help="Plus minus positions for the same PTM site."/>
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206 </when>
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207
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208 <!-- Proteins -->
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209 <when value="uniprot">
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210 <param format="txt" name="input_uniprot" type="data" label="UniProt Accession list"
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211 help="File with a one Uniprot Accession [4] in each line."/>
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212 </when>
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213
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214 <when value="ensembl">
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215 <param format="txt" name="input_ensembl" type="data" label="Ensembl identifier list"
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216 help="File with a one Ensembl identifier [5] in each line."/>
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217 </when>
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218
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219 <!-- Proteoforms -->
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220 <when value="proteoforms">
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221 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"
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222 help="A proteoform defines a specific state of a protein.
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223 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
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224 The input file contains one line for each proteoform. Each PTM is specified using a modification
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225 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
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226 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
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227
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228 <param name="proteoform_match_criteria" type="select" label="Proteoform match criteria">
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229 <option value="STRICT">STRICT</option>
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230 <option value="ONE">ONE</option>
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231 <option value="SUPERSET" selected="True">SUPERSET</option>
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232 <option value="SUBSET">SUBSET</option>
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233 </param>
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234 </when>
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235
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236 </conditional>
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237
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238 </repeat>
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239
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240 <section name="output_options" expanded="true" title="Output options">
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241
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242 <param name="search_top_level_info" type="select" label="Add search top level info">
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243 <option value="0" selected="True">False</option>
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244 <option value="1">True</option>
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245 </param>
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246
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247 <param name="output_graphs" type="select" display="checkboxes" multiple="True" label="Connection graphs"
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248 help="Generates a zipped file with connection graphs as an additional output when executing the pathway search and analysis.
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249 The graph can use genes, proteins or proteoforms as vertices.">
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250 <option value="gg">Genes</option>
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251 <option value="gu">Proteins</option>
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252 <option value="gp">Proteoforms</option>
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253 </param>
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254
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255 </section>
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256
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257 </inputs>
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258 <outputs>
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259 <data name="search" format="tsv" from_work_dir="search.tsv" label="${tool.name} - search on ${on_string}" />
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260 <data name="analysis" format="tsv" from_work_dir="analysis.tsv" label="${tool.name} - analysis on ${on_string}" />
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261 <collection name="graphs_files" type="list" label="${tool.name} - graphs on ${on_string}" >
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262 <filter>output_options['output_graphs'] != None</filter>
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263 <discover_datasets pattern="__name_and_ext__" directory="graphs" ext="tsv"/>
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264 </collection>
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265 </outputs>
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266
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267
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268 <tests>
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269
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270 <!-- Test that genes search works -->
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271 <test>
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272 <repeat name="input_types">
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273 <conditional name="input_type">
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274 <param name="input_type_selector" value="gene"/>
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275 <param name="input_gene" value="genes.txt" ftype="txt" />
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276 </conditional>
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277 </repeat>
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278 <output name="search" file="genes_search.tsv" ftype="tsv" compare="sim_size" delta="3000" />
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279 </test>
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280
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281 <!-- Test graphs from proteoforms -->
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282 <test>
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283 <repeat name="input_types">
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284 <conditional name="input_type">
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285 <param name="input_type_selector" value="proteoforms"/>
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286 <param name="input_proteoforms" value="proteoforms.txt" ftype="txt" />
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287 </conditional>
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288 </repeat>
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289 <param name="output_graphs" value="gg,gu,gp" />
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290 <output_collection name="graphs_files" type="list">
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291 <element name="geneExternalEdges" ftype="tsv" file="proteoforms_graphs/geneExternalEdges.tsv" compare="sim_size" delta="1000" />
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292 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="1000"/>
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293 <element name="geneVertices" ftype="tsv" file="proteoforms_graphs/geneVertices.tsv" compare="sim_size" delta="1000"/>
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294 <element name="proteinExternalEdges" ftype="tsv" file="proteoforms_graphs/proteinExternalEdges.tsv" compare="sim_size" delta="10000"/>
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295 <element name="proteinInternalEdges" ftype="tsv" file="proteoforms_graphs/proteinInternalEdges.tsv" compare="sim_size" delta="1000"/>
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296 <element name="proteinVertices" ftype="tsv" file="proteoforms_graphs/proteinVertices.tsv" compare="sim_size" delta="1000"/>
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297 <element name="proteoformExternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformExternalEdges.tsv" compare="sim_size" delta="1000"/>
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298 <element name="proteoformInternalEdges" ftype="tsv" file="proteoforms_graphs/proteoformInternalEdges.tsv" compare="sim_size" delta="1000"/>
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299 <element name="proteoformVertices" ftype="tsv" file="proteoforms_graphs/proteoformVertices.tsv" compare="sim_size" delta="1000"/>
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300 </output_collection>
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301 </test>
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302
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303 </tests>
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304 <help>
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305
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306 .. class:: infomark
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307
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308 **Introduction**
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309
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310 Biological pathways are an excellent resource to analyze the causes and consequences of certain phenotypes.
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311 Most of the components of the pathways are proteins. When searching for relevant pathways to perform analysis
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312 of a patient sample proteins, it is very common to lose information due to lack of precision in the search.
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313
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314 This leads to result sets with many extra selected pathways that are not really related to the input sample.
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315
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316 .. class:: infomark
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317
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318 **What it does**
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319
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320 We present more fine grained approach to search, not only with the gene names, but also with post translational
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321 modifications of the proteins, such as phosphorylation.
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322
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323 Ultimately, any omics dataset with its mutations and
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324 modifications will be mapped directly to the functional knowledgebases allowing the functional interpretation by
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325 researchers and clinicians.
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326
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327 The reference database used is Reactome, a free, open source, curated and peer reviewed database of biological reactions, that contains the quality data needed for this type of fine grained search. database of biological reactions. It can be readily queried with omics datasets, and we are improving its features by extending the matching the clinical data to the biological pathways. Not only will the gene names be used, but also mutations or post translational modifications such as phosphorylation.
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328
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329
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330 .. class:: infomark
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331
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332 **Inputs and outputs**
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333
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334 PathwayMatcher can search for reactions and pathways with various input types, and generates mapping files to the database.
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335
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336 The input can be:
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337
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338 - Genetic variants
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339 - Genes
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340 - Peptides
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341 - Protein
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342 - Proteoforms
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343
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344 The output of PathwayMatcher is composed of two files, the Reaction and Pathway mapping and the statistical analysis of the relevant pathways.
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345
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346 .. class:: infomark
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347
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348 Information included with this tool is a brief summary of the main one included in PathwayMatcher_.
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349
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350 Specific information about PathwayMatcher's Input_ and Output_ may also be found there.
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351
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352
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353 .. class:: infomark
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354
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355 **References**
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356
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357 [1] dbSNP_
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358
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359 [2] VCF v4.3:
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360 http://samtools.github.io/hts-specs/VCFv4.3.pdf
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361
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362 [3] genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1079-85. doi: 10.1093/nar/gku1071. :
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363 https://www.ncbi.nlm.nih.gov/pubmed/25361968
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364
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365 [4] UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017):
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366 http://dx.doi.org/doi:10.1093/nar/gkw1099
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367
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368 [5] Ensembl:
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369 https://www.ensembl.org/info/genome/stable_ids/index.html
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370
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371 [6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008):
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372 http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html
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373
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374 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
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375 .. _PathwayMatcher: https://github.com/LuisFranciscoHS/PathwayMatcher
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376 .. _Input: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Input
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377 .. _Output: https://github.com/LuisFranciscoHS/PathwayMatcher/wiki/Output
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378
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379 </help>
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380
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381 </tool>