# HG changeset patch # User iuc # Date 1604096321 0 # Node ID caf213d51d6cea672c0d93a6f17ddf76f5181af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7" diff -r 000000000000 -r caf213d51d6c README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Oct 30 22:18:41 2020 +0000 @@ -0,0 +1,20 @@ +# PyEGA3 + +## Set up user credentials on Galaxy + +To enable users to set their credentials for this tool, +make sure the file `config/user_preferences_extra.yml` has the following section: + +``` + ega_account: + description: Your EGA (European Genome Archive) account + inputs: + - name: username + label: Username + type: text + required: False + - name: password + label: Password + type: password + required: False +``` diff -r 000000000000 -r caf213d51d6c pyega3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyega3.xml Fri Oct 30 22:18:41 2020 +0000 @@ -0,0 +1,138 @@ + + + 3.4.0 + + + pyega3 + + Preferences -> Manage Information" && + +#if $action.action_type == "list_datasets" + pyega3 -cf '$credentials' + datasets +#elif $action.action_type == "list_dataset_files" + pyega3 -cf '$credentials' + files '$action.dataset_id' +#elif $action.action_type == "download_file" + pyega3 -cf '$credentials' + fetch '$action.file_id' + #if $action.range.reference_name + --reference-name '$action.range.reference_name' + #if $action.range.start + --start $action.range.start + #end if + #if $action.range.end + --end $action.range.end + #end if + #end if + --saveto '$downloaded_file' +#end if + ]]> + + + + + + + + + + + + + EGAD[0-9]+ + + + + + + EGAF[0-9]+ + +
+ + + +
+
+
+
+ + + action['action_type'] == 'list_datasets' + + + action['action_type'] == 'list_dataset_files' + + + action['action_type'] == 'download_file' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1038/ng.3312 + +