Mercurial > repos > goeckslab > rename_tiff_channels

annotate rename_tiff_channels.xml @ 6:4763362914f4 draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 5c324d06ad54dca76aa2b4c8118df5654f49da66
author goeckslab
date Mon, 15 Jul 2024 21:37:39 +0000
parents 61fd94c7ce42
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
goeckslab
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1 <tool id="rename_tiff_channels" name="Rename OME-TIFF channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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2 <description>with ome-types</description>
0
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3 <macros>
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4 <import>macros.xml</import>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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5 </macros>
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d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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7 <edam_operations>
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8 <edam_operation>operation_3443</edam_operation>
d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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9 </edam_operations>
d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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10
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18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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11 <expand macro="requirements"/>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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13 <stdio>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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14 <regex match=".*XMLSyntaxError.*"
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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15 source="stderr"
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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16 level="fatal"
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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17 description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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18 </stdio>
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20 <expand macro="version_cmd"/>
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0
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22 <command detect_errors="aggressive"><![CDATA[
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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24 cp '$image' ./renamed_image.ome.tiff &&
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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26 ln -s '$channel_csv' ./channels.csv &&
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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28 python '$script'
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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30 ]]></command>
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31 <configfiles>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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32 <configfile name = "script">
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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33 import os
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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34 import sys
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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35 import argparse
5
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36 from itertools import cycle
0
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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37 import pandas as pd
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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38 import ome_types
5
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39 from ome_types.model import channel, Color
0
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40 from tifffile import tiffcomment
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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41
5
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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42 # setting default colors to match avivator
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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43 colors = [
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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44 (0,0,255,1.0), # blue
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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45 (0,255,0,1.0), # green
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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46 (255,0,255,1.0), # magenta
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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47 (255,255,0,1.0), # yellow
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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48 (255,127,0,1.0), # orange
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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49 (0,255,255,1.0), # cyan
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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50 (255,255,255,1.0), # white
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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51 (255,0,0,1.0) # red
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52 ]
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53
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54 # convert to repeatable object of primitive int colors
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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55 color_cycle = cycle([Color(c).as_int32() for c in colors])
61fd94c7ce42 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
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56
0
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57 cwd = os.getcwd()
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18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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59 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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61 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))
6
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62 working_ome = ome_types.from_xml(original_ome_xml)
0
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64 for l_idx, level in enumerate(working_ome.images):
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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65
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66 for c_idx, channel in enumerate(level.pixels.channels):
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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67
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68 new_name = channels_df.loc[c_idx, 'marker_name']
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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69 channel.name = new_name
5
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70 channel.color = next(color_cycle)
0
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72 if l_idx == 0:
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74 print(f"Channel {c_idx} renamed to {new_name}")
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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75
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76 updated_ome_xml = working_ome.to_xml().encode()
0
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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77 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml)
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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79 print("Updated OME-TIFF metadata:")
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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80 print(tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff')))
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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81 </configfile>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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82 </configfiles>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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83 <inputs>
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84 <param name="image" type="data" format="ome.tiff" label="Input image in OME-tiff format"/>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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85 <param name="channel_csv" type="data" format="csv" label="Channel Metadata CSV"/>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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86 </inputs>
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87 <outputs>
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88 <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="image" value="rename_test.ome.tiff" />
0
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93 <param name="channel_csv" value="rename_channels.csv" />
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94 <output name="renamed_image" ftype="ome.tiff">
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95 <assert_contents>
6
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96 <has_size value="900000" delta="50000" />
0
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97 </assert_contents>
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98 </output>
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99 <assert_stdout>
6
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100 <has_text text="Channel 0 renamed to Hematoxylin" />
0
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101 <has_text text="Updated OME-TIFF metadata" />
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102 <has_text text="µm" />
0
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103 </assert_stdout>
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104 </test>
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105 </tests>
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106 <help><![CDATA[
2
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107 Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the
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108 OME XML metadata. CSV file must contain column 'marker_name' which will populate the XML
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109 metadata with channel names in the order provided in the CSV file.
0
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110 ]]></help>
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111 <expand macro="citations" />
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112 </tool>