Mercurial > repos > iuc > ncbi_eutils_epost
diff epost.xml @ 8:acb271106065 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
| author | iuc |
|---|---|
| date | Wed, 23 Sep 2020 09:46:35 +0000 |
| parents | a640698e77d9 |
| children | 8fb2684407cc |
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--- a/epost.xml Wed Mar 11 07:54:00 2020 +0000 +++ b/epost.xml Wed Sep 23 09:46:35 2020 +0000 @@ -6,29 +6,97 @@ </macros> <expand macro="requirements"/> <version_command>python epost.py --version</version_command> - <command detect_errors="aggressive"><![CDATA[ -python '$__tool_directory__/epost.py' -$db_select + <command detect_errors="aggressive"> + <![CDATA[ + + python '$__tool_directory__/epost.py' + + $db_select + + @EMAIL_ARGUMENTS@ -@EMAIL_ARGUMENTS@ + #if $query_source.qss == "id_file": + --id_list $query_source.id_file + #else if $query_source.qss == "id_list": + --id $query_source.id_list + #else if $query_source.qss == "id_xml": + --id_xml $query_source.id_xml + #else if $query_source.qss == "id_json": + --id_json $query_source.id_json + #end if + + #if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_json": + --history_file "$update_history.history_entry.history_file" + #else if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_xml": + --history_xml "$update_history.history_entry.history_xml" + #else if $update_history.history_type == "paste": + --webenv "$update_history.webenv" + #end if + + > $history -@LIST_OR_HIST@ + ]]> + </command> + <inputs> + <conditional name="query_source"> + <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable. Query IDs in an ELink result are ignored."> + <option value="id_file" selected="True">ID file (Tabular)</option> + <option value="id_xml">ID File (XML)</option> + <option value="id_json">ID File (JSON)</option> + <option value="id_list">Paste IDs</option> + </param> + <when value="id_file"> + <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/> + </when> + <when value="id_xml"> + <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/> + </when> + <when value="id_json"> + <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/> + </when> + <when value="id_list"> + <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> + </when> + </conditional> + + <expand macro="dbselect"/> -> $history -]]></command> - <inputs> - <expand macro="dbselect"/> - <expand macro="list_or_hist"/> + <conditional name="update_history"> + <param name="history_type" type="select" label="Target History" help="IDs will be saved to a supplied or created history."> + <option value="create" selected="True">Create a new history</option> + <option value="select">Add to an existing history by file</option> + <option value="paste">Add to an existing history by history (WebEnv) ID</option> + </param> + <when value="create"/> + <when value="select"> + <conditional name="history_entry"> + <param name="history_select" type="select" label="Select an existing history"> + <option value="history_json">History File (JSON)</option> + <option value="history_xml">History File (XML)</option> + </param> + <when value="history_json"> + <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID referencing the history on the NCBI history server to which to add the IDs"/> + </when> + <when value="history_xml"> + <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID referencing the history on the NCBI history server to which to add the IDs"/> + </when> + </conditional> + </when> + <when value="paste"> + <param name="webenv" type="text" label="WebEnv History ID"/> + </when> + </conditional> </inputs> <outputs> - <expand macro="history_out"/> + <data format="json" name="history" label="NCBI History"/> </outputs> <tests> <test> <param name="db_select" value="nuccore"/> <param name="qss" value="id_list"/> <param name="id_list" value="126697566"/> - <output name="history" file="example.history.json" compare="sim_size" delta="10" ftype="json"/> + <param name="history_type" value="create"/> + <output name="history" file="example.history.json" compare="sim_size" delta="70" ftype="json"/> </test> </tests> <help><