Mercurial > repos > galaxyp > reactome_pathwaymatcher
comparison pathwaymatcher.xml @ 6:622dd6d51032 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher commit 421ada25856b841ce17949e80eb3a47fa276a967"
| author | galaxyp |
|---|---|
| date | Mon, 06 Apr 2020 19:18:34 -0400 |
| parents | a2ab72e994dc |
| children |
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| 5:a2ab72e994dc | 6:622dd6d51032 |
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| 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. |