diff alveo_data_importer.xml @ 14:a38315ecf593 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/alveo_data_importer.xml	Wed Nov 01 01:18:15 2017 -0400
@@ -0,0 +1,54 @@
+<tool id="alveo_data_importer" name="Get Item URLs for Item List + API Key" version="0.01">
+    <description>Stores API Key and Retrieves Item URLs from an Alveo Item List
+        Version called directly from the Alveo web application
+    </description>
+
+    <requirements>
+        <requirement type="package" version="0.7">pyalveo</requirement>
+    </requirements>
+
+    <command interpreter="python">
+        alveo_data_importer.py --api_key $api_key --item_list_url $item_list --outputkey $outputkey --output $output
+    </command>
+
+    <inputs>
+        <param name="api_key" type="text" size="30" label="API Key" help="Your Alveo API key"/>
+        <param name="item_list" type="text" label="Alveo Item List URL" help="The Alveo Item List you wish to import"/>
+        <param name="job_name" type="text" size="25"
+               label="Supply a name for the outputs to remind you what they contain" value="Item List"/>
+    </inputs>
+
+    <outputs>
+        <data format="auth_token" name="outputkey" label="Alveo API key" />
+        <data format="item_list" name="output" label="${job_name}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <!-- expect this to fail unless you enter a valid API key here and copy it to
+                     the result file -->
+            <param name="api_key" value="your api key here" />
+
+            <param name="import_list" value="item-lists.dat"/>
+            <param name="item_list_url" value="https://app.alveo.edu.au/item_lists/180"/>
+            <param name="job_name" value="test_output_180.dat"/>
+            <output name="outputkey" file="api-key.dat" compare="contains" />
+            <output name="output" file="item_list_180.dat"/>
+        </test>
+    </tests>
+
+    <help>Store an API Key and get the URLs of all of the items from an Alveo item list.
+    This is a combination of the "Store Alveo API Key" and "Get Item URLs for Item List"
+    tools written so that it can be called directly from the Alveo web application
+    item list page.</help>
+    <citations>
+        <citation type='bibtex'>
+            @article{cassidy2014alveo,
+              title={The {Alveo Virtual Laboratory}: a web based repository API},
+              author={Cassidy, Steve and Estival, Dominique and Jones, Tim and Sefton, Peter and Burnham, Denis and Burghold, Jared and others},
+              year={2014},
+              publisher={Reykjavik, Iceland: European Language Resources Association}
+            }
+        </citation>
+    </citations>
+</tool>