Mercurial > repos > galaxyp > reactome_pathwaymatcher

comparison pathwaymatcher.xml @ 6:b43dec819c48 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967"
author galaxyp
date Mon, 06 Apr 2020 23:18:10 +0000
parents 00ee806dd5ff
children
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5:00ee806dd5ff 6:b43dec819c48
2 <description> 2 <description>
3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. 3 PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome.
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token> 6 <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token>
7 <token name="@TOOL_SUBVERSION@">3</token> 7 <token name="@TOOL_SUBVERSION@">4</token>
8 <xml name="input_fasta"> 8 <xml name="input_fasta">
9 <param format="fasta" name="input_database" type="data" label="Protein Database" 9 <param format="fasta" name="input_database" type="data" label="Protein Database"
10 help="Select FASTA database from history"/> 10 help="Select FASTA database from history"/>
11 </xml> 11 </xml>
12 </macros> 12 </macros>
13 <requirements> 13 <requirements>
14 <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement> 14 <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement>
15 <requirement type="package" version="3.0">zip</requirement> 15 <requirement type="package" version="3.0">zip</requirement>
16 <requirement type="package" version="8.31">coreutils</requirement>
16 </requirements> 17 </requirements>
17 <stdio> 18 <stdio>
18 <exit_code range="1:" level="fatal" description="Job Failed" /> 19 <exit_code range="1:" level="fatal" description="Job Failed" />
19 <regex match="java.*Exception" level="fatal" description="Java Exception"/> 20 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
20 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> 21 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
35 export HOME=\$cwd; 36 export HOME=\$cwd;
36 37
37 ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files. 38 ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files.
38 #for $i, $s in enumerate($match_types) 39 #for $i, $s in enumerate($match_types)
39 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms" 40 #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms"
40 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './'; 41 unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './' &&
41 mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt; 42 mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt &&
42 #end if 43 #end if
43 #end for 44 #end for
44 45
45 ##################### 46 #####################
46 ## Pathway Matcher ## 47 ## Pathway Matcher ##
47 ##################### 48 #####################
48 (pathwaymatcher 49 pathwaymatcher
49 50
50 #for $i, $s in enumerate($match_types) 51 #for $i, $s in enumerate($match_types)
51
52 ## PROTEOFORMS 52 ## PROTEOFORMS
53 53
54 #if $s.match_type.match_type_selector == "proteoforms" 54 #if $s.match_type.match_type_selector == "proteoforms"
55 #if $s.match_type.proteoform_match_criteria: 55 #if $s.match_type.proteoform_match_criteria:
56 match-proteoforms -m '${s.match_type.proteoform_match_criteria}' -i '${s.match_type.input_proteoforms}' -r '${s.match_type.proteoform_range}' 56 match-proteoforms -m '${s.match_type.proteoform_match_criteria}' -i '${s.match_type.input_proteoforms}' -r '${s.match_type.proteoform_range}'
114 match-modified-peptides -i '${s.match_type.input_modifiedpeptide}' 114 match-modified-peptides -i '${s.match_type.input_modifiedpeptide}'
115 -f '${s.match_type.input_database}' 115 -f '${s.match_type.input_database}'
116 -m '${s.match_type.modifiedpeptide_match_criteria}' 116 -m '${s.match_type.modifiedpeptide_match_criteria}'
117 -r '${s.match_type.modifiedpeptide_ptm_range}' 117 -r '${s.match_type.modifiedpeptide_ptm_range}'
118 #end if 118 #end if
119
120
121 #end for 119 #end for
122 120
123 ## OUTPUT OPTIONS 121 ## OUTPUT OPTIONS
124 122
125 #if $output_options.search_top_level_info: 123 #if $output_options.search_top_level_info:
138 136
139 #if 'gp' in $output_graphs_list: 137 #if 'gp' in $output_graphs_list:
140 -gp 138 -gp
141 #end if 139 #end if
142 140
143 2>> $temp_stderr);
144
145 ## We create a folder to contain graphs files. 141 ## We create a folder to contain graphs files.
146 #if $output_options.output_graphs: 142 #if $output_options.output_graphs:
147 mkdir "graphs"; 143 && mkdir "graphs"
148 #end if 144 #end if
149 #if 'gg' in $output_graphs_list: 145 #if 'gg' in $output_graphs_list:
150 mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ; 146 && mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv"
151 #end if 147 #end if
152 #if 'gu' in $output_graphs_list: 148 #if 'gu' in $output_graphs_list:
153 mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv"; 149 && mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv"
154 #end if 150 #end if
155 #if 'gp' in $output_graphs_list: 151 #if 'gp' in $output_graphs_list:
156 mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv"; 152 && mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv"
157 #end if 153 #end if
158
159 exit_code_for_galaxy=\$?;
160 cat $temp_stderr 2>&1;
161 (exit \$exit_code_for_galaxy)
162 ]]> 154 ]]>
163 </command> 155 </command>
164 <inputs> 156 <inputs>
165
166 <repeat name="match_types" title="Match" min="1"> 157 <repeat name="match_types" title="Match" min="1">
167 <conditional name="match_type"> 158 <conditional name="match_type">
168 <param name="match_type_selector" type="select" label="Match type" 159 <param name="match_type_selector" type="select" label="Match type"
169 help=""> 160 help="">
170 <option value="proteoforms">Proteoforms</option> 161 <option value="proteoforms">Proteoforms</option>
176 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option> 167 <option value="chrbp">Genetic variants - Chromosomes and base pairs</option>
177 <option value="rsid">Genetic variants - SNP rsId list</option> 168 <option value="rsid">Genetic variants - SNP rsId list</option>
178 <option value="peptide">Peptides - Simple list</option> 169 <option value="peptide">Peptides - Simple list</option>
179 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option> 170 <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option>
180 </param> 171 </param>
181
182 172
183 <!-- Proteoforms --> 173 <!-- Proteoforms -->
184 <when value="proteoforms"> 174 <when value="proteoforms">
185 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms" 175 <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"
186 help="A proteoform defines a specific state of a protein. 176 help="A proteoform defines a specific state of a protein.