changeset 2:28fc15925666 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"

--- a/data_manager/funannotate.py	Thu Nov 18 21:49:27 2021 +0000
+++ b/data_manager/funannotate.py	Fri Nov 19 11:15:26 2021 +0000
@@ -224,6 +224,7 @@
 
     parser = argparse.ArgumentParser()
     parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
+    parser.add_argument('--wget', dest='wget', action='store_true', help='Download using wget (instead of urllib)')
     parser.add_argument("version_id")
     parser.add_argument("datatable_name")
     parser.add_argument("galaxy_datamanager_filename")
@@ -243,6 +244,8 @@
     cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
     if args.partial:
         cmd_args += ['-i', 'merops', '-b', 'eukaryota']
+    if args.wget:
+        cmd_args += ['--wget']
     proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
     return_code = proc.wait()
     if return_code:

--- a/data_manager/funannotate.xml	Thu Nov 18 21:49:27 2021 +0000
+++ b/data_manager/funannotate.xml	Fri Nov 19 11:15:26 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.2" tool_type="manage_data" profile="20.01">
+<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01">
     <requirements>
         <requirement type="package" version="1.8.9">funannotate</requirement>
         <requirement type="package" version="2.26.0">requests</requirement>
@@ -7,12 +7,14 @@
     <command detect_errors="exit_code"><![CDATA[
 python -u '$__tool_directory__/funannotate.py'
 $partial_data
+$wget
 \$(date +'%Y-%m-%d-%H%M%S')
 'funannotate'
 '${output_file}'
     ]]></command>
     <inputs>
         <param name="partial_data" type="hidden" value="" help="Used for testing"/>
+        <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json"/>
@@ -27,6 +29,16 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="partial_data" value="--partial"/>
+            <param name="wget" value="True"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="Funannotate database "/>
+                    <has_text text='"format_version": "1.0"'/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
         This data managers fetches data from various databases for the funannotate