Mercurial > repos > thanhlv > ariba
changeset 10:9c6408c3ae01 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ariba commit 8742424d7265fc71164db9a65f15583993a90b52-dirty
| author | thanhlv |
|---|---|
| date | Tue, 25 Jun 2019 08:52:55 -0400 |
| parents | 6b44bd3c8ebc |
| children | e613afbb9e7a |
| files | ariba_summary.xml |
| diffstat | 1 files changed, 9 insertions(+), 7 deletions(-) [+] |
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--- a/ariba_summary.xml Mon May 13 05:22:44 2019 -0400 +++ b/ariba_summary.xml Tue Jun 25 08:52:55 2019 -0400 @@ -16,11 +16,12 @@ #set $named_input_files = '' #for $input_file in $ariba_reports ## Add single quotes around each input file identifier - #set $_input_file = "'{}'".format($input_file.element_identifier) + ##set $_input_file = "'{}'".format($input_file.element_identifier) + #set $_input_file = re.sub('[^\w\-_\.]', '_', $input_file.element_identifier) ln -s '${input_file}' ${_input_file} && #set $named_input_files = $named_input_files + ' ' + $_input_file #end for - ariba summary out + ariba summary --preset $options.preset @@ -29,9 +30,10 @@ #end if --min_id $options.min_id + out - $named_input_files - > $log + '$named_input_files' + ]]> </command> <inputs> <param name="ariba_reports" format="tabular,txt" type="data" multiple="true" label="Report (tsv) file from ARIBA run" help="This command requires one or more report tsv file generated by ARIBA run command."/> @@ -50,9 +52,9 @@ <outputs> <data name="log" format="tabular" label="${tool.name} on ${on_string} log file"/> - <data name="summary_csv" format="tabular" label="${tool.name} on ${on_string} report file" from_work_dir="out.tsv" /> - <data name="phandango_csv" format="tabular" label="${tool.name} on ${on_string}: Phandango CSV" from_work_dir="out.phandango.csv" /> - <data name="phandango_tree" format="text" label="${tool.name} on ${on_string}: Phandango Tree file" from_work_dir="out.phandango.tre"> + <data name="summary_csv" format="tabular" label="${tool.name} on ${on_string} report file" from_work_dir="out.csv" /> + <data name="phandango_csv" format="csv" label="${tool.name} on ${on_string}: Phandango CSV" from_work_dir="out.phandango.csv" /> + <data name="phandango_tree" format="tre" label="${tool.name} on ${on_string}: Phandango Tree file" from_work_dir="out.phandango.tre"> <filter>no_tree is False</filter> </data> </outputs>