changeset 0:fe887de9b4b5 draft

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zipcollection.py	Thu Nov 16 06:19:53 2017 -0500
@@ -0,0 +1,28 @@
+from __future__ import print_function
+import argparse
+from zipfile import ZipFile
+
+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('--output', required=True, action="store", type=str, help="Path to output file")
+    return parser.parse_args()
+
+
+def main():
+    args = parser()
+
+    datasets = args.dataset.split(',')
+    identifiers = args.identifier.split(',')
+    assert len(datasets) == len(identifiers), "number of datasets must match number of identifiers"
+
+    pairs = zip(datasets, identifiers)
+
+    with ZipFile(args.output, 'w') as zipfile:
+        for dataset, identifier in pairs:
+            zipfile.write(dataset, identifier)
+
+
+if __name__ == '__main__':
+    main()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/zipcollection.xml	Thu Nov 16 06:19:53 2017 -0500
@@ -0,0 +1,31 @@
+<tool id="zipcollection" name="Create a Zip file" version="0.01">
+    <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 $output
+    </command>
+
+    <inputs>
+        <param name="dataset" format="data" type="data"
+               multiple="true" label="DataSets" help="Datasets to include in zip"/>
+        <param name="job_name" type="text" size="25"
+               label="Name of output zip file" value="dataset"/>
+    </inputs>
+
+    <outputs>
+        <data format="zip" name="output" label="$job_name" />
+    </outputs>
+
+    <tests>
+        <!-- can't compare zip file as it changes based on time the test is run
+        <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"/>
+        </test>
+        -->
+    </tests>
+
+    <help>Creates a zip file from a dataset or dataset collection</help>
+
+</tool>