Mercurial > repos > stevecassidy > ziptools
changeset 1:278da6e5ab11 draft default tip
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit f2432aaedd36ae7662873623d8861d0982dffdd2
author | stevecassidy |
---|---|
date | Mon, 20 Nov 2017 22:51:12 -0500 |
parents | fe887de9b4b5 |
children | |
files | zipcollection.py zipcollection.xml |
diffstat | 2 files changed, 22 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/zipcollection.py Thu Nov 16 06:19:53 2017 -0500 +++ b/zipcollection.py Mon Nov 20 22:51:12 2017 -0500 @@ -1,11 +1,14 @@ from __future__ import print_function import argparse from zipfile import ZipFile +import os + def parser(): parser = argparse.ArgumentParser(description="Find matching segments in a TextGrid") parser.add_argument('--dataset', required=True, action="store", type=str, help="TextGrid files (comma separated)") parser.add_argument('--identifier', required=True, action="store", type=str, help="Dataset identifiers (comma separated)") + parser.add_argument('--extension', required=False, action='store', default='', type=str, help="Extension for stored files") parser.add_argument('--output', required=True, action="store", type=str, help="Path to output file") return parser.parse_args() @@ -21,7 +24,15 @@ with ZipFile(args.output, 'w') as zipfile: for dataset, identifier in pairs: - zipfile.write(dataset, identifier) + + # rewrite extension if asked + if args.extension != '': + base, ext = os.path.splitext(identifier) + outname = base + "." + args.extension + else: + outname = identifier + + zipfile.write(dataset, outname) if __name__ == '__main__':
--- a/zipcollection.xml Thu Nov 16 06:19:53 2017 -0500 +++ b/zipcollection.xml Mon Nov 20 22:51:12 2017 -0500 @@ -2,12 +2,19 @@ <description>from one or more datasets</description> <command interpreter="python"> - zipcollection.py --dataset "${",".join(map(str, $dataset))}" --identifier "${",".join(map(str, [t.element_identifier + "." + t.extension for t in $dataset]))}" --output $output + zipcollection.py --dataset "${",".join(map(str, $dataset))}" + --identifier "${",".join(map(str, [t.element_identifier + "." + t.extension for t in $dataset]))}" + #if $extension: + --extension $extension + #end if + --output $output </command> <inputs> <param name="dataset" format="data" type="data" multiple="true" label="DataSets" help="Datasets to include in zip"/> + <param name="extension" type="text" size="10" format="text" + label="New extension for files (leave empty to use the dataset type, eg txt, tabbed)"/> <param name="job_name" type="text" size="25" label="Name of output zip file" value="dataset"/> </inputs> @@ -21,9 +28,9 @@ <test> <param name="dataset" value="textgrids/1_1308_2_22_020-ch6-speaker16.TextGrid_TextGrid"/> <param name="job_name" value="test.zip"/> - <output name="output" ftype="zip"/> + <output name="output" ftype="zip" file="test.zip"/> </test> - --> + --> </tests> <help>Creates a zip file from a dataset or dataset collection</help>