Mercurial > repos > ufz > omero_get_value
changeset 4:7a94eb8c345d draft default tip
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 6f47dff3775455a8c45d39a3863a2306cd942443
| author | ufz |
|---|---|
| date | Tue, 08 Apr 2025 15:13:16 +0000 |
| parents | ecb13e93fae2 |
| children | |
| files | omero_get_value.py omero_get_value.xml |
| diffstat | 2 files changed, 103 insertions(+), 22 deletions(-) [+] |
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--- a/omero_get_value.py Thu Dec 19 14:57:46 2024 +0000 +++ b/omero_get_value.py Tue Apr 08 15:13:16 2025 +0000 @@ -1,15 +1,17 @@ import argparse import csv import json +import os import sys import ezomero as ez +import pandas as pd -def get_object_ezo(user, pws, host, port, obj_type, ids, tsv_file): +def get_object_ezo(user, pws, host, port, obj_type, ids, out_dir): # Function to write tabular file from the ezomero output def write_values_to_tsv(data, header): - with open(tsv_file, 'w', newline='') as f: + with open("output.tsv", 'w', newline='') as f: writer = csv.writer(f, delimiter='\t') writer.writerow([header]) # Write the header for item in data: @@ -17,15 +19,15 @@ # Function to write tabular file from a dictionary ezomero output def write_dict_to_tsv(data, headers): - with open(tsv_file, 'w', newline='') as f: + with open("output.tsv", 'w', newline='') as f: writer = csv.writer(f, delimiter='\t') writer.writerow(headers) # Write the headers for key, value in data.items(): writer.writerow([key, value]) # Write each key-value pair # Function to write tabular file from list of list ezomero output - def write_table_to_tsv(data): - with open(tsv_file, 'w') as f: + def write_table_to_tsv(data, id): + with open(f"./output/ID_{id}_table.tsv", 'w') as f: for row in data: f.write('\t'.join([str(val) for val in row]) + '\n') @@ -35,8 +37,8 @@ for maid in ids: current_ma_dict = ez.get_map_annotation(conn, maid) ma_dict = {**ma_dict, **current_ma_dict} + print(ma_dict) write_dict_to_tsv(ma_dict, ["Annotation ID", "Annotation Value"]) - return ma_dict elif obj_type == "Tag": tags = [] for tag_id in ids: @@ -44,14 +46,18 @@ # Sort the tags for consistency: tags.sort write_values_to_tsv(tags, "Tags") - return tags elif obj_type == "Table": - if len(ids) > 1: - raise ValueError("Only one table can be exported at a time") - table = ez.get_table(conn, ids[0]) - write_table_to_tsv(table) - return table - + for id in ids: + table = ez.get_table(conn, id) + print(table) + write_table_to_tsv(table, id) + elif obj_type == ("Attachment"): + for id in ids: + attch_path = ez.get_file_annotation(conn, id, folder_path='./output/') + base_name = os.path.basename(attch_path) + df = pd.read_csv(attch_path, sep='\t') + df.to_csv(f"./output/ID_{id}_{base_name}", sep='\t', index=False) + os.remove(attch_path) else: sys.exit(f"Unsupported object type: {filter}") @@ -72,8 +78,8 @@ help="IDs of the OMERO objects.") group.add_argument('--ids_path', help="File with IDs of the OMERO objects (one per line).") - parser.add_argument('--tsv_file', default='id_list.tsv', required=True, - help="Output TSV file path.") + parser.add_argument('--out_dir', required=True, + help="Output path.") args = parser.parse_args() if args.ids_path: @@ -95,4 +101,4 @@ port=args.port, obj_type=args.obj_type, ids=args.ids, - tsv_file=args.tsv_file) + out_dir=args.out_dir)
--- a/omero_get_value.xml Thu Dec 19 14:57:46 2024 +0000 +++ b/omero_get_value.xml Tue Apr 08 15:13:16 2025 +0000 @@ -2,13 +2,14 @@ <description> with ezomero </description> <macros> <import>macros.xml</import> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <xrefs> <xref type="bio.tools">omero</xref> </xrefs> <expand macro="ezomero_requirements"/> <command detect_errors="exit_code"><![CDATA[ + mkdir output; python '$__tool_directory__/omero_get_value.py' --credential-file '$credentials' @HOST_PORT@ @@ -18,7 +19,7 @@ #else --ids_path '$ids_input.ids_path' #end if - --tsv_file '$tsv' + --out_dir ./output/ ]]></command> <configfiles> <expand macro="credentials"/> @@ -29,6 +30,7 @@ <option value="Annotation">Annotation</option> <option value="Tag">Tag</option> <option value="Table">Table</option> + <option value="Attachment">Attachment</option> </param> <conditional name="ids_input"> <param name="ids_format" type="select" label="How do you provide the ID(s) of the OMERO object?"> @@ -46,10 +48,16 @@ </conditional> </inputs> <outputs> - <data name="tsv" format="tabular"/> + <collection name="split_output" type="list"> + <discover_datasets pattern="__name_and_ext__" directory="output"/> + <filter> not (obj_type=="Tag" or obj_type=="Annotation")</filter> + </collection> + <data name="tsv" from_work_dir="output.tsv" format="tabular"> + <filter> obj_type=="Tag" or obj_type=="Annotation"</filter> + </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="omero_host" value="host.docker.internal"/> <param name="omero_port" value="6064"/> <param name="obj_type" value="Tag"/> @@ -66,12 +74,79 @@ </assert_contents> </output> </test> + <test expect_num_outputs="1"> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <param name="obj_type" value="Annotation"/> + <conditional name="ids_input"> + <param name="ids_format" value="values"/> + <param name="ids" value="7"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="tsv" ftype="tabular"> + <assert_contents> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <param name="obj_type" value="Attachment"/> + <conditional name="ids_input"> + <param name="ids_format" value="values"/> + <param name="ids" value="2,3,4"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output_collection name="split_output" type="list" count="3"> + <element name="ID_2_attachment"> + <assert_contents> + <has_text text="col1"/> + </assert_contents> + </element> + <element name="ID_3_attachment"> + <assert_contents> + <has_text text="col1"/> + </assert_contents> + </element> + <element name="ID_4_attachment"> + <assert_contents> + <has_text text="col1"/> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="1"> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <param name="obj_type" value="Table"/> + <conditional name="ids_input"> + <param name="ids_format" value="values"/> + <param name="ids" value="5,6"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output_collection name="split_output" type="list" count="2"> + <element name="ID_5_table"> + <assert_contents> + <has_n_lines n="5"/> + </assert_contents> + </element> + <element name="ID_6_table"> + <assert_contents> + <has_n_lines n="5"/> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help> Description ----------- -Tool to fetch Annotation, Tag and Tables from IDs. +Tool to fetch Annotation, Tag, Tables and Attachments from IDs. The IDs can be obtained with the tool OMERO get IDs with ezomero @@ -80,4 +155,4 @@ <citations> <citation type="doi">10.1038/nmeth.1896</citation> </citations> -</tool> \ No newline at end of file +</tool>