Mercurial > repos > goeckslab > rename_tiff_channels

annotate rename_tiff_channels.xml @ 2:d2c59a1ac0c4 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
author goeckslab
date Wed, 28 Feb 2024 20:52:08 +0000
parents 18f6be63414c
children 61fd94c7ce42
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1 <tool id="rename_tiff_channels" name="Rename OME-TIFF channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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>
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5 </macros>
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7 <edam_operations>
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8 <edam_operation>operation_3443</edam_operation>
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9 </edam_operations>
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0
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11 <expand macro="requirements"/>
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13 <stdio>
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14 <regex match=".*XMLSyntaxError.*"
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15 source="stderr"
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16 level="fatal"
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17 description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
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18 </stdio>
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19
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20 <expand macro="version_cmd"/>
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0
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22 <command detect_errors="aggressive"><![CDATA[
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24 cp '$image' ./renamed_image.ome.tiff &&
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26 ln -s '$channel_csv' ./channels.csv &&
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28 python '$script'
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30 ]]></command>
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31 <configfiles>
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32 <configfile name = "script">
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33 import os
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34 import sys
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35 import argparse
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36 import pandas as pd
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37 import ome_types
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38 from ome_types.model import channel
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39 from tifffile import tiffcomment
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41 cwd = os.getcwd()
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43 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
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45 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))
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46 working_ome = ome_types.from_xml(original_ome_xml, parser = 'lxml')
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47
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48 for l_idx, level in enumerate(working_ome.images):
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50 for c_idx, channel in enumerate(level.pixels.channels):
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51
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52 new_name = channels_df.loc[c_idx, 'marker_name']
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53 channel.name = new_name
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54
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55 if l_idx == 0:
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56
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57 print(f"Channel {c_idx} renamed to {new_name}")
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59 updated_ome_xml = working_ome.to_xml()
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60 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml)
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61
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62 print("Updated OME-TIFF metadata:")
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63 print(tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff')))
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64 </configfile>
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65 </configfiles>
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66 <inputs>
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67 <param name="image" type="data" format="ome.tiff" label="Input image in OME-tiff format"/>
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68 <param name="channel_csv" type="data" format="csv" label="Channel Metadata CSV"/>
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69 </inputs>
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70 <outputs>
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71 <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="image" value="rename_test.tiff" />
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76 <param name="channel_csv" value="rename_channels.csv" />
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77 <output name="renamed_image" ftype="ome.tiff">
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78 <assert_contents>
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79 <has_size value="44000" delta="1000" />
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80 </assert_contents>
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81 </output>
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82 <assert_stdout>
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83 <has_text text="Channel 0 renamed to DNA_6" />
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84 <has_text text="Updated OME-TIFF metadata" />
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85 </assert_stdout>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89 Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the
d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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90 OME XML metadata. CSV file must contain column 'marker_name' which will populate the XML
d2c59a1ac0c4 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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91 metadata with channel names in the order provided in the CSV file.
0
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92 ]]></help>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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93 <expand macro="citations" />
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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94 </tool>