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Commit message:
planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/defense-finder commit 71a859e126c239a33ed9fee014330c8ae820ae3c |
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modified:
defense_finder.xml |
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| diff -r 9dbeaec173b5 -r 596fa7bf596f defense_finder.xml --- a/defense_finder.xml Thu Mar 07 15:57:42 2024 +0000 +++ b/defense_finder.xml Thu Mar 07 16:45:46 2024 +0000 |
| [ |
| @@ -1,14 +1,13 @@ <tool id="defense_finder" name="DefenseFinder" version="@TOOL_VERSION@+@WRAPPER_VERSION@" python_template_version="3.5" profile="21.05"> <description>systematically detect known anti-phage systems</description> <macros> - <token name="@WRAPPER_VERSION@">galaxy0</token> + <token name="@WRAPPER_VERSION@">galaxy1</token> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ mkdir tmp-models && - echo ${models.fields.path} && ln -s '${models.fields.path}' 'tmp-models/${models.fields.value}' && ln -s '${genome}' '${genome.name}' && defense-finder run '${genome.name}' @@ -16,6 +15,7 @@ --workers \${GALAXY_SLOTS:-1} --db-type '${db_type}' --coverage '${coverage}' + -o out ${preserve_raw} ${no_cut_ga} ]]></command> @@ -37,10 +37,10 @@ <param argument="--preserve-raw" type="boolean" truevalue="--preserve-raw" falsevalue="" label="Preserve raw MacsyFinder outputs" help="Preserve raw MacsyFinder outputs alongside Defense Finder results inside the output directory"/> </inputs> <outputs> - <data format="tabular" name="genes" from_work_dir="*_defense_finder_genes.tsv" label="${tool.name} on ${on_string}: genes"/> - <data format="tabular" name="hmmer" from_work_dir="*_defense_finder_hmmer.tsv" label="${tool.name} on ${on_string}: hmmer"/> - <data format="tabular" name="systems" from_work_dir="*_defense_finder_systems.tsv" label="${tool.name} on ${on_string}: systems"/> - <data format="fasta" name="proteins" from_work_dir="*.prt" label="${tool.name} on ${on_string}: proteins" /> + <data format="tabular" name="genes" from_work_dir="out/*_defense_finder_genes.tsv" label="${tool.name} on ${on_string}: genes"/> + <data format="tabular" name="hmmer" from_work_dir="out/*_defense_finder_hmmer.tsv" label="${tool.name} on ${on_string}: hmmer"/> + <data format="tabular" name="systems" from_work_dir="out/*_defense_finder_systems.tsv" label="${tool.name} on ${on_string}: systems"/> + <data format="fasta" name="proteins" from_work_dir="out/*.prt" label="${tool.name} on ${on_string}: proteins" /> </outputs> <tests> <test> |