Mercurial > repos > galaxyp > reactome_pathwaymatcher

annotate pathwaymatcher.xml @ 4:3e510701a712 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
author galaxyp
date Sun, 14 Jul 2019 05:09:33 -0400
parents 2cd67294abbd
children a2ab72e994dc
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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>
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6 <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>
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7 <token name="@TOOL_SUBVERSION@">2</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 <regex match="filename not matched: reports/proteins_proteoforms.txt" level="fatal" description="PeptideShaker archive does not contain the proteoforms file. It may have been created by a 1.x PeptideShaker version."/>
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22 </stdio>
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23 <command>
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24 <![CDATA[
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25 #from datetime import datetime
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26 #import json
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27 #import os
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28 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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29 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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30 #set $temp_stderr = "pathwaym_stderr"
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31 #set $bin_dir = "bin"
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32
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33 mkdir output;
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34 cwd=`pwd`;
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35 export HOME=\$cwd;
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36
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37 ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files.
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38 #for $i, $s in enumerate($match_types)
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39 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
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40 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './';
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41 mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt;
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42 #end if
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43 #end for
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44
0
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45 #####################
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46 ## Pathway Matcher ##
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47 #####################
3
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48 (pathwaymatcher
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49
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50 #for $i, $s in enumerate($match_types)
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51
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52 ## PROTEOFORMS
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53
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54 #if $s.match_type.match_type_selector == "proteoforms"
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55 #if $s.match_type.proteoform_match_criteria:
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56 match-proteoforms -m '${s.match_type.proteoform_match_criteria}' -i '${s.match_type.input_proteoforms}' -r '${s.match_type.proteoform_range}'
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57 #else:
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58 match-proteoforms -i '${s.match_type.input_proteoforms}' -r '${s.match_type.proteoform_range}'
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59 #end if
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60 #end if
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61
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62 ## PROTEOFORMS FROM PEPTIDESHAKER FILE
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63
3
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64 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
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65 #if $s.match_type.proteoform_peptideshakerzip_match_criteria:
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66 match-proteoforms -m '${s.match_type.proteoform_peptideshakerzip_match_criteria}' -i ps_proteoforms_'${$i}'.txt -r '${s.match_type.proteoform_peptideshakerzip_range}'
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67 #else:
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68 match-proteoforms -i ps_proteoforms_'${$i}'.txt -r '${s.match_type.proteoform_peptideshakerzip_range}'
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69 #end if
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70 #end if
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73 ## GENES
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75 #if $s.match_type.match_type_selector == "gene"
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76 match-genes -i '${s.match_type.input_gene}'
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77 #end if
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80 ## PROTEINS
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82 #if $s.match_type.match_type_selector == "uniprot"
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83 match-uniprot -i '${s.match_type.input_uniprot}'
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84 #end if
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85
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86 #if $s.match_type.match_type_selector == "ensembl"
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87 match-ensembl -i '${s.match_type.input_ensembl}'
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88 #end if
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89
0
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90
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91 ## GENETIC VARIANTS
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92
3
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93 #if $s.match_type.match_type_selector == "vcf"
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94 match-vcf -i '${s.match_type.input_vcf}'
0
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95 #end if
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96
3
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97 #if $s.match_type.match_type_selector == "chrbp"
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98 match-chrbp -i '${s.match_type.input_chrbp}'
0
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99 #end if
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100
3
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101 #if $s.match_type.match_type_selector == "rsid"
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102 match-rsids -i '${s.match_type.input_rsid}'
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103 #end if
0
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104
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105
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106 ## PEPTIDES
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107
3
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108 #if $s.match_type.match_type_selector == "peptide"
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109 match-peptides -i '${s.match_type.input_peptide}'
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110 -f '${s.match_type.input_database}'
0
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111 #end if
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112
3
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113 #if $s.match_type.match_type_selector == "modifiedpeptide"
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114 match-modified-peptides -i '${s.match_type.input_modifiedpeptide}'
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115 -f '${s.match_type.input_database}'
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116 -m '${s.match_type.modifiedpeptide_match_criteria}'
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117 -r '${s.match_type.modifiedpeptide_ptm_range}'
0
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118 #end if
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119
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120
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121 #end for
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122
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123 ## OUTPUT OPTIONS
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124
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125 #if $output_options.search_top_level_info:
3
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126 -T
0
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127 #end if
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128
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129 #set $output_graphs_list = str($output_options.output_graphs).split(',')
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130
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131 #if 'gg' in $output_graphs_list:
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132 -gg
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133 #end if
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134
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135 #if 'gu' in $output_graphs_list:
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136 -gu
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137 #end if
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138
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139 #if 'gp' in $output_graphs_list:
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140 -gp
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141 #end if
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142
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143 2>> $temp_stderr);
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144
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145 ## We create a folder to contain graphs files.
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146 #if $output_options.output_graphs:
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147 mkdir "graphs";
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148 #end if
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149 #if 'gg' in $output_graphs_list:
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150 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ;
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151 #end if
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152 #if 'gu' in $output_graphs_list:
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153 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv";
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154 #end if
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155 #if 'gp' in $output_graphs_list:
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156 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv";
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157 #end if
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158
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159 exit_code_for_galaxy=\$?;
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160 cat $temp_stderr 2>&1;
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161 (exit \$exit_code_for_galaxy)
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162 ]]>
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163 </command>
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164 <inputs>
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165
3
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166 <repeat name="match_types" title="Match" min="1">
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167 <conditional name="match_type">
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168 <param name="match_type_selector" type="select" label="Match type"
0
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169 help="">
3
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170 <option value="proteoforms">Proteoforms</option>
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171 <option value="peptideshakerzip_proteoforms">Proteoforms from Peptideshaker 2.x Archive</option>
3
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172 <option value="gene">Genes</option>
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173 <option value="uniprot">Proteins - UniProt Accession list</option>
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174 <option value="ensembl">Proteins - Ensembl identifier list</option>
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175 <option value="vcf">Genetic variants - Variant Call Format Specification</option>
0
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176 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
3
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177 <option value="rsid">Genetic variants - SNP rsId list</option>
0
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178 <option value="peptide">Peptides - Simple list</option>
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179 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
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180 </param>
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181
3
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182
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183 <!-- Proteoforms -->
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184 <when value="proteoforms">
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185 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"
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186 help="A proteoform defines a specific state of a protein.
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187 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
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188 The input file contains one line for each proteoform. Each PTM is specified using a modification
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189 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
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190 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
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191
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192 <param name="proteoform_match_criteria" type="select" label="Proteoform match criteria">
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193 <option value="STRICT">STRICT</option>
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194 <option value="SUPERSET">SUPERSET</option>
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195 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
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196 <option value="SUBSET" selected="True">SUBSET</option>
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197 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
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198 <option value="ONE">ONE</option>
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199 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
4
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200 <option value="ACCESSION">ACCESSION</option>
3
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201 </param>
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202
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203 <param name="proteoform_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true"
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204 help="Plus minus positions for the same PTM site"/>
0
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205 </when>
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206
3
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207 <when value="peptideshakerzip_proteoforms">
4
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208 <param format="zip" name="input_peptideshakerzip_proteoforms" type="data" label="Proteoforms from Peptideshaker 2.x Archive"
3
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209 help="A proteoform defines a specific state of a protein.
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210 It is composed by the protein UniProt accession, isoform and set of post translational modifications.
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211 The input file contains one line for each proteoform. Each PTM is specified using a modification
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212 identifier and a site, separated by ':'(semicolon). For example: '00046:133'.
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213 The identifier is a 5 digit id from the PSI-MOD Protein Modification Onthology [6]."/>
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214
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215 <param name="proteoform_peptideshakerzip_match_criteria" type="select" label="Proteoform match criteria">
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216 <option value="STRICT">STRICT</option>
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217 <option value="SUPERSET">SUPERSET</option>
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218 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
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219 <option value="SUBSET" selected="True">SUBSET</option>
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220 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
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221 <option value="ONE">ONE</option>
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222 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
4
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223 <option value="ACCESSION">ACCESSION</option>
3
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224 </param>
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225
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226 <param name="proteoform_peptideshakerzip_range" type="integer" value="0" label="Integer range of error for PTM sites" optional="true"
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227 help="Plus minus positions for the same PTM site"/>
0
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228 </when>
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229
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230
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231 <!-- Genes -->
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232 <when value="gene">
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233 <param format="txt" name="input_gene" type="data" label="Genes"
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234 help="File with a one gene name in each line. Genes follow the HUGO gene nomenclature[3]."/>
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235 </when>
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236
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237
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238 <!-- Proteins -->
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239 <when value="uniprot">
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240 <param format="txt" name="input_uniprot" type="data" label="UniProt Accession list"
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241 help="File with a one Uniprot Accession [4] in each line."/>
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242 </when>
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243
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244 <when value="ensembl">
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245 <param format="txt" name="input_ensembl" type="data" label="Ensembl identifier list"
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246 help="File with a one Ensembl identifier [5] in each line."/>
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247 </when>
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248
3
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249 <!-- Genetic variants -->
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250
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251 <when value="vcf">
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252 <param format="vcf" name="input_vcf" type="data" label="Variant Call Format Specification"
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253 help="The input follows the Variant Call Format Specification[2] v4.3.
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254 It also allows the possibility to specify only the first 4 columns in the data section of the file:
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255 CHROM, POS, ID, REF. "/>
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256 </when>
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257
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258 <when value="chrbp">
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259 <param format="txt" name="input_chrbp" type="data" label="Chromosomes and base pairs"
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260 help="Genetic variants can also be represented using the chromosome and the base pair numbers.
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261 The input should be sorted by chromosome number and then by base pair. "/>
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262 </when>
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263
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264 <when value="rsid">
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265 <param format="txt" name="input_rsid" type="data" label="SNP rsId list"
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266 help="The file contains one rsid identifier as defined in dbSNP[1] on each row.
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267 The list must be ordered by chromosome and base pair (bp). The list must not have duplicates.
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268 All rsids must appear in the human assembly GRCh37.p13. "/>
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269 </when>
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270
0
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271
3
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272 <!-- Peptides -->
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273 <when value="peptide">
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274 <param format="txt" name="input_peptide" type="data" label="Simple list"
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275 help="File with a one peptide sequence in each line."/>
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276
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277 <expand macro="input_fasta" />
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278
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279 </when>
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280
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281 <when value="modifiedpeptide">
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282 <param format="txt" name="input_modifiedpeptide" type="data" label="Peptide List with PTM types and sites"
2cd67294abbd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
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283 help="Each line of the file corresponds to a single peptide with post-translational modifications."/>
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284
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285 <expand macro="input_fasta" />
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286
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287 <param name="modifiedpeptide_match_criteria" type="select" label="Proteoform match criteria. Only modified peptides.">
0
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288 <option value="STRICT">STRICT</option>
3
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289 <option value="SUPERSET">SUPERSET</option>
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290 <option value="SUPERSET_NO_TYPES">SUPERSET NO TYPES</option>
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291 <option value="SUBSET" selected="True">SUBSET</option>
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292 <option value="SUBSET_NO_TYPES">SUBSET NO TYPES</option>
0
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293 <option value="ONE">ONE</option>
3
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294 <option value="ONE_NO_TYPES">ONE_NO_TYPES</option>
4
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295 <option value="ACCESSION">ACCESSION</option>
0
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296 </param>
3
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297
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298 <param name="modifiedpeptide_ptm_range" type="integer" value="0" label="PTM position range" optional="true"
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299 help="Integer number margin error for sites of PTMs. Only for modified peptides."/>
0
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300 </when>
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301
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302 </conditional>
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303
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304 </repeat>
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305
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306 <section name="output_options" expanded="true" title="Output options">
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307
3
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308 <param name="search_top_level_info" type="select" label="Add Top Level Pathways in the search result.">
0
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309 <option value="0" selected="True">False</option>
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310 <option value="1">True</option>
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311 </param>
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312
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313 <param name="output_graphs" type="select" display="checkboxes" multiple="True" label="Connection graphs"
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314 help="Generates a zipped file with connection graphs as an additional output when executing the pathway search and analysis.
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315 The graph can use genes, proteins or proteoforms as vertices.">
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316 <option value="gg">Genes</option>
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317 <option value="gu">Proteins</option>
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318 <option value="gp">Proteoforms</option>
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319 </param>
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320
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321 </section>
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322
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323 </inputs>
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324 <outputs>
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325 <data name="search" format="tsv" from_work_dir="search.tsv" label="${tool.name} - search on ${on_string}" />
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326 <data name="analysis" format="tsv" from_work_dir="analysis.tsv" label="${tool.name} - analysis on ${on_string}" />
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327 <collection name="graphs_files" type="list" label="${tool.name} - graphs on ${on_string}" >
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328 <filter>output_options['output_graphs'] != None</filter>
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329 <discover_datasets pattern="__name_and_ext__" directory="graphs" ext="tsv"/>
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330 </collection>
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331 </outputs>
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332
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333
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334 <tests>
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335
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336 <!-- Test that genes search works -->
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337 <test>
3
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338 <repeat name="match_types">
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339 <conditional name="match_type">
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340 <param name="match_type_selector" value="gene"/>
0
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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341 <param name="input_gene" value="genes.txt" ftype="txt" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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342 </conditional>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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343 </repeat>
4
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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344 <output name="search" ftype="tsv" >
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345 <assert_contents>
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346 <has_line_matching expression="CFTR\tP13569\tR-HSA-383190\tHCO3- transport through ion channel\tR-HSA-382556\tABC-family proteins mediated transport\tR-HSA-382551\tTransport of small molecules"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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347 <has_line_matching expression="TGFB1\tP01137\tR-HSA-170850\tPhosphorylated SMAD2/3 dissociates from TGFBR\tR-HSA-170834\tSignaling by TGF-beta Receptor Complex\tR-HSA-162582\tSignal Transduction"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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348 <has_line_matching expression="SCNN1B\tP51168\tR-HSA-2682349\tRAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels\tR-HSA-382551\tTransport of small molecules\tR-HSA-382551\tTransport of small molecules"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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349 <has_line_matching expression="TNFRSF1A\tP19438\tR-HSA-5626988\tTNF-alpha:TNFR1 binds NSMAF\tR-HSA-75893\tTNF signaling\tR-HSA-162582\tSignal Transduction"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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350 <has_n_columns n="8" />
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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351 </assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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352 </output>
0
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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353 </test>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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354
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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355 <!-- Test graphs from proteoforms -->
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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356 <test>
3
2cd67294abbd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
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357 <repeat name="match_types">
2cd67294abbd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
galaxyp
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358 <conditional name="match_type">
2cd67294abbd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
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359 <param name="match_type_selector" value="proteoforms"/>
0
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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360 <param name="input_proteoforms" value="proteoforms.txt" ftype="txt" />
3
2cd67294abbd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 79d03b32b395b4c1385ff934251b17ea8950187b
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361 <param name="proteoform_match_criteria" value="SUBSET"/>
0
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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362 </conditional>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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363 </repeat>
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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364 <param name="output_graphs" value="gg,gu,gp" />
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
galaxyp
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365 <output_collection name="graphs_files" type="list">
4
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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366 <element name="geneExternalEdges" ftype="tsv">
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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367 <assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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368 <has_line_matching expression="ERBB4\tSRC\tReaction\tR-HSA-1963586\tcatalyst\tcatalyst"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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369 <has_line_matching expression="RNF85\tSRC1\tReaction\tR-HSA-2316434\tcatalyst\tcatalyst"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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370 <has_line_matching expression="CBL2\tUNQ2500/PRO5800\tReaction\tR-HSA-5654677\tinput\tinput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
371 <has_line_matching expression="FN1\tPRKM3\tReaction\tR-HSA-5672973\tcatalyst\toutput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
372 <has_line_matching expression="MAPK11\tMAPK12\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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373 <has_line_matching expression="SAPK2B\tSAPK3\tSet\tR-HSA-448855\tmember/candidate\tmember/candidate"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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374 <has_n_columns n="6" />
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
375 </assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
376 </element>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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diff changeset
377 <element name="geneInternalEdges" ftype="tsv" file="proteoforms_graphs/geneInternalEdges.tsv" compare="sim_size" delta="10"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
378 <element name="geneVertices" ftype="tsv">
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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379 <assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
380 <has_line_matching expression="ERK1\tMitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
381 <has_line_matching expression="CREB1\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
382 <has_line_matching expression="SAPK2\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
383 <has_line_matching expression="STAT5\tSignal transducer and activator of transcription 5A ]"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
384 <has_n_columns n="2" />
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
385 </assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
386 </element>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
387 <element name="proteinExternalEdges" ftype="tsv">
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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388 <assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
389 <has_line_matching expression="P12931\tP56975\tReaction\tR-HSA-1963586\tcatalyst\toutput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
390 <has_line_matching expression="P12931\tP51617\tReaction\tR-HSA-2316434\tcatalyst\tregulator"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
391 <has_line_matching expression="P12931\tQ8N302\tReaction\tR-HSA-6802933\tcatalyst\tinput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
392 <has_line_matching expression="O95352\tP12931\tComplex\tR-HSA-6802695\tcomponent\tcomponent"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
393 <has_line_matching expression="Q15759\tQ16539\tSet\tR-HSA-198703\tmember/candidate\tmember/candidate"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
394 <has_n_columns n="6" />
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
395 </assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
396 </element>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
397 <element name="proteinInternalEdges" ftype="tsv">
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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398 <assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
399 <has_line_matching expression="P00519\tP12931\tReaction\tR-HSA-8942607\tcatalyst\tcatalyst"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
400 <has_line_matching expression="P12931\tQ9UQC2\tReaction\tR-HSA-205234\toutput\toutput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
401 <has_line_matching expression="P12931\tP27361\tReaction\tR-HSA-6802933\tinput\toutput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
402 <has_line_matching expression="P12931\tP27361\tReaction\tR-HSA-6802910\tinput\tinput"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
403 <has_line_matching expression="P00519\tP12931\tSet\tR-HSA-8942611\tmember/candidate\tmember/candidate"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
404 <has_line_matching expression="P12931\tP42229\tComplex\tR-HSA-1469999\tcomponent\tcomponent"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
405 <has_n_columns n="6" />
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
406 </assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
407 </element>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
408 <element name="proteinVertices" ftype="tsv">
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
409 <assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
410 <has_line_matching expression="P16220\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
411 <has_line_matching expression="P27361\tMitogen-activated protein kinase 3 shortName:MAP kinase 3 shortName:MAPK 3 ecNumber2.7.11.24/ecNumber"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
412 <has_line_matching expression="P42229\tSignal transducer and activator of transcription 5A ]"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
parents: 3
diff changeset
413 <has_n_columns n="2" />
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
414 </assert_contents>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
415 </element>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
416 <element name="proteoformExternalEdges" ftype="tsv">
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
galaxyp
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diff changeset
417 <assert_contents>
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418 <has_line_matching expression="O43597;00048:55,00048:227\tP22681;\tComplex\tR-HSA-934576\tcomponent\tcomponent"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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419 <has_line_matching expression="P00533;00048:992,00048:1045,00048:1068,00048:1086,00048:1148,00048:1173\tP22681;\tComplex\tR-HSA-182935\tcomponent\tcomponent"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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420 <has_line_matching expression="P27361;00047:202,00048:204\tP28482;00047:185,00048:187\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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421 <has_line_matching expression="P12931;00048:419\tQ01196;\tComplex\tR-HSA-8937687\tcomponent\tcomponent"/>
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422 <has_line_matching expression="P15509;\tP42229;00048:694\tSet\tR-HSA-913465\tmember/candidate\tmember/candidate"/>
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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423 <has_n_columns n="6" />
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424 </assert_contents>
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425 </element>
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426 <element name="proteoformInternalEdges" ftype="tsv">
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427 <assert_contents>
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428 <has_line_matching expression="P27361;00047:202,00048:204\tQ15759;00047:180,00048:182\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
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429 <has_line_matching expression="P27361;00047:202,00048:204\tQ15759;00047:180,00048:182\tSet\tR-HSA-450307\tmember/candidate\tmember/candidate"/>
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430 <has_n_columns n="6" />
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431 </assert_contents>
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432 </element>
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433 <element name="proteoformVertices" ftype="tsv">
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434 <assert_contents>
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435 <has_line_matching expression="P16220;00046:133\tCyclic AMP-responsive element-binding protein 1 shortName:CREB-1 shortName:cAMP-responsive element-binding protein 1 ]"/>
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436 <has_line_matching expression="Q15759;00047:180,00048:182\tMitogen-activated protein kinase 11 shortName:MAP kinase 11 shortName:MAPK 11 ecNumber2.7.11.24/ecNumber"/>
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437 <has_line_matching expression="P42229;00048:694\tSignal transducer and activator of transcription 5A ]"/>
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438 <has_n_columns n="2" />
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439 </assert_contents>
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440 </element>
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441
0
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442 </output_collection>
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443 </test>
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444
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445 </tests>
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446 <help>
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447
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448 .. class:: infomark
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449
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450 **Introduction**
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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451
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452 Biological pathways are an excellent resource to analyze the causes and consequences of certain phenotypes.
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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453 Most of the components of the pathways are proteins. When searching for relevant pathways to perform analysis
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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454 of a patient sample proteins, it is very common to lose information due to lack of precision in the search.
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455
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456 This leads to result sets with many extra selected pathways that are not really related to the input sample.
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457
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458 .. class:: infomark
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459
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460 **What it does**
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461
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462 We present more fine grained approach to search, not only with the gene names, but also with post translational
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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463 modifications of the proteins, such as phosphorylation.
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464
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465 Ultimately, any omics dataset with its mutations and
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466 modifications will be mapped directly to the functional knowledgebases allowing the functional interpretation by
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467 researchers and clinicians.
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468
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469 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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470
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471
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472 .. class:: infomark
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473
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474 **Inputs and outputs**
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475
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476 PathwayMatcher can search for reactions and pathways with various input types, and generates mapping files to the database.
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477
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478 The input can be:
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479
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480 - Genetic variants
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481 - Genes
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482 - Peptides
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483 - Protein
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484 - Proteoforms
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485
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486 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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487
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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488 .. class:: infomark
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489
2
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490 **Try it now**
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491
4
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492 You can easily test PathwayMatcher functionality creating text files with the example data we provide with proteoforms and proteins information of Cystic Fibrosis:
2
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493
4
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494 **Proteoforms**:
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495
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496 ::
2
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497
4
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498 P01137;
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499 P10145;
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500 P12318;
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501 P12318;00048:288,00048:304
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502 P13569;
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503 P13569;01148:null
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504 P19438;
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505 P37088;
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506 P37088;01148:null
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507 P51168;
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508 P51170;
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509 P51170;01148:null
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510 Q14CN2;
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511 Q16623;
3e510701a712 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 1d08bec4a320f62652392f08c2481bbe215e37fa
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512 Q9UJW0;
2
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513
4
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514 **Proteins**:
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515 ::
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516
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517 P13569
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518 P01137
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519 P12318
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520 Q9UJW0
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521 P51168
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522 P51170
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523 P37088
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524 P19438
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525 Q14CN2
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526 Q16623
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527 P10145
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528
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529 After copying and pasting this data into new text files, you can upload them to Galaxy by directly using the Galaxy upload dialog (the button with the arrow pointing up in the top-left area, and then choosing *Choose local file*).
2
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530
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531 Once they appear in green in your history, they have been uploaded and you can use them as inputs in PathwayMatcher.
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532
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533 Now, select *Proteoforms* as input type and, in the next drop-down list, the entry of your history corresponding to the proteoforms file you uploaded.
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534
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535 Then, click on *insert input* to add a new PathwayMatcher input for the proteins. Select *Proteins - Uniprot accession list* as input type and, in the next drop-down list, the entry in your history corresponding to this proteins file.
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536
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537 **Everything is ready**. By clicking on *Execute* PathwayMatcher will run with your chosen inputs and, after a short time, it will show in your history two more files with the search results and its analysis.
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538
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539 .. class:: infomark
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540
0
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541 Information included with this tool is a brief summary of the main one included in PathwayMatcher_.
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542
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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543 Specific information about PathwayMatcher's Input_ and Output_ may also be found there.
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544
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545 .. class:: infomark
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546
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547 **References**
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548
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549 [1] dbSNP_
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550
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551 [2] VCF v4.3:
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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552 http://samtools.github.io/hts-specs/VCFv4.3.pdf
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553
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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554 [3] genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1079-85. doi: 10.1093/nar/gku1071. :
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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555 https://www.ncbi.nlm.nih.gov/pubmed/25361968
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556
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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557 [4] UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45: D158-D169 (2017):
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558 http://dx.doi.org/doi:10.1093/nar/gkw1099
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559
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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560 [5] Ensembl:
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561 https://www.ensembl.org/info/genome/stable_ids/index.html
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562
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563 [6] The PSI-MOD community standard for representation of protein modification data. Nature Biotechnology 26, 864 - 866 (2008):
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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564 http://www.nature.com/nbt/journal/v26/n8/full/nbt0808-864.html
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565
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566 .. _dbSNP: https://www.ncbi.nlm.nih.gov/projects/SNP/
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567 .. _PathwayMatcher: https://github.com/PathwayAnalysisPlatform/PathwayMatcher
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568 .. _Input: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Input
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569 .. _Output: https://github.com/PathwayAnalysisPlatform/PathwayMatcher/wiki/Output
0
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570
f66af2b04a98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit c12a99d3da62c83b779175b3c9022e7d5622053a
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571 </help>
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572
3
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573 <citations>
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574 <citation type="doi">doi:10.1101/375097</citation>
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575 </citations>
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576
0
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577 </tool>