Mercurial > repos > goeckslab > rename_tiff_channels

comparison rename_tiff_channels.xml @ 0:18f6be63414c draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
author goeckslab
date Thu, 29 Sep 2022 16:53:36 +0000
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children d2c59a1ac0c4
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-1:000000000000 0:18f6be63414c
1 <tool id="rename_tiff_channels" name="Rename OME-TIFF Channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Change the channel names in the XML metadata of OME-TIFF images</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements"/>
8 <expand macro="version_cmd"/>
9
10 <stdio>
11 <regex match=".*XMLSyntaxError.*"
12 source="stderr"
13 level="fatal"
14 description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
15 </stdio>
16
17 <command detect_errors="aggressive"><![CDATA[
18
19 cp '$image' ./renamed_image.ome.tiff &&
20
21 ln -s '$channel_csv' ./channels.csv &&
22
23 python '$script'
24
25 ]]></command>
26 <configfiles>
27 <configfile name = "script">
28 import os
29 import sys
30 import argparse
31 import pandas as pd
32 import ome_types
33 from ome_types.model import channel
34 from tifffile import tiffcomment
35
36 cwd = os.getcwd()
37
38 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
39
40 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))
41 working_ome = ome_types.from_xml(original_ome_xml, parser = 'lxml')
42
43 for l_idx, level in enumerate(working_ome.images):
44
45 for c_idx, channel in enumerate(level.pixels.channels):
46
47 new_name = channels_df.loc[c_idx, 'marker_name']
48 channel.name = new_name
49
50 if l_idx == 0:
51
52 print(f"Channel {c_idx} renamed to {new_name}")
53
54 updated_ome_xml = working_ome.to_xml()
55 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml)
56
57 print("Updated OME-TIFF metadata:")
58 print(tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff')))
59 </configfile>
60 </configfiles>
61 <inputs>
62 <param name="image" type="data" format="ome.tiff" label="Input image in OME-tiff format"/>
63 <param name="channel_csv" type="data" format="csv" label="Channel Metadata CSV"/>
64 </inputs>
65 <outputs>
66 <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
67 </outputs>
68 <tests>
69 <test>
70 <param name="image" value="rename_test.tiff" />
71 <param name="channel_csv" value="rename_channels.csv" />
72 <output name="renamed_image" ftype="ome.tiff">
73 <assert_contents>
74 <has_size value="44000" delta="1000" />
75 </assert_contents>
76 </output>
77 <assert_stdout>
78 <has_text text="Channel 0 renamed to DNA_6" />
79 <has_text text="Updated OME-TIFF metadata" />
80 </assert_stdout>
81 </test>
82 </tests>
83 <help><![CDATA[
84 ]]></help>
85 <expand macro="citations" />
86 </tool>