Mercurial > repos > galaxyp > reactome_pathwaymatcher
changeset 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 | |
| files | pathwaymatcher.xml |
| diffstat | 1 files changed, 9 insertions(+), 19 deletions(-) [+] |
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--- a/pathwaymatcher.xml Sun Aug 04 15:52:53 2019 -0400 +++ b/pathwaymatcher.xml Mon Apr 06 19:18:34 2020 -0400 @@ -4,7 +4,7 @@ </description> <macros> <token name="@PATHWAYMATCHER_VERSION@">1.9.1</token> - <token name="@TOOL_SUBVERSION@">3</token> + <token name="@TOOL_SUBVERSION@">4</token> <xml name="input_fasta"> <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history"/> @@ -13,6 +13,7 @@ <requirements> <requirement type="package" version="@PATHWAYMATCHER_VERSION@">pathwaymatcher</requirement> <requirement type="package" version="3.0">zip</requirement> + <requirement type="package" version="8.31">coreutils</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> @@ -37,18 +38,17 @@ ## If we use peptideshaker 2.x files as inputs, firstly we need to uncompress their proteoforms files. #for $i, $s in enumerate($match_types) #if $s.match_type.match_type_selector == "peptideshakerzip_proteoforms" - unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './'; - mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt; + unzip -j '${$s.match_type.input_peptideshakerzip_proteoforms}' 'reports/proteins_proteoforms.txt' -d './' && + mv proteins_proteoforms.txt ps_proteoforms_'${$i}'.txt && #end if #end for ##################### ## Pathway Matcher ## ##################### - (pathwaymatcher + pathwaymatcher #for $i, $s in enumerate($match_types) - ## PROTEOFORMS #if $s.match_type.match_type_selector == "proteoforms" @@ -116,8 +116,6 @@ -m '${s.match_type.modifiedpeptide_match_criteria}' -r '${s.match_type.modifiedpeptide_ptm_range}' #end if - - #end for ## OUTPUT OPTIONS @@ -140,29 +138,22 @@ -gp #end if - 2>> $temp_stderr); - ## We create a folder to contain graphs files. #if $output_options.output_graphs: - mkdir "graphs"; + && mkdir "graphs" #end if #if 'gg' in $output_graphs_list: - mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" ; + && mv -t "graphs" "geneExternalEdges.tsv" "geneInternalEdges.tsv" "geneVertices.tsv" #end if #if 'gu' in $output_graphs_list: - mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv"; + && mv -t "graphs" "proteinExternalEdges.tsv" "proteinInternalEdges.tsv" "proteinVertices.tsv" #end if #if 'gp' in $output_graphs_list: - mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv"; + && mv -t "graphs" "proteoformExternalEdges.tsv" "proteoformInternalEdges.tsv" "proteoformVertices.tsv" #end if - - exit_code_for_galaxy=\$?; - cat $temp_stderr 2>&1; - (exit \$exit_code_for_galaxy) ]]> </command> <inputs> - <repeat name="match_types" title="Match" min="1"> <conditional name="match_type"> <param name="match_type_selector" type="select" label="Match type" @@ -179,7 +170,6 @@ <option value="modifiedpeptide">Peptides - Peptide List with PTM types and sites</option> </param> - <!-- Proteoforms --> <when value="proteoforms"> <param format="txt" name="input_proteoforms" type="data" label="Proteoforms"