Mercurial > repos > goeckslab > rename_tiff_channels

annotate 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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18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
goeckslab
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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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goeckslab
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2 <description>Change the channel names in the XML metadata of OME-TIFF images</description>
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3 <macros>
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goeckslab
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4 <import>macros.xml</import>
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goeckslab
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5 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_cmd"/>
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10 <stdio>
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11 <regex match=".*XMLSyntaxError.*"
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12 source="stderr"
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13 level="fatal"
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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14 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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15 </stdio>
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17 <command detect_errors="aggressive"><![CDATA[
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19 cp '$image' ./renamed_image.ome.tiff &&
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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21 ln -s '$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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23 python '$script'
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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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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25 ]]></command>
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goeckslab
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26 <configfiles>
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27 <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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28 import os
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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29 import sys
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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30 import argparse
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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31 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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32 import ome_types
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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33 from ome_types.model import channel
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34 from tifffile import tiffcomment
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36 cwd = os.getcwd()
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38 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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39
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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40 original_ome_xml = 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
goeckslab
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41 working_ome = ome_types.from_xml(original_ome_xml, parser = 'lxml')
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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43 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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18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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45 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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18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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47 new_name = channels_df.loc[c_idx, 'marker_name']
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48 channel.name = new_name
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49
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50 if l_idx == 0:
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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51
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52 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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53
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54 updated_ome_xml = working_ome.to_xml()
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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55 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml)
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56
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57 print("Updated OME-TIFF metadata:")
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58 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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59 </configfile>
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60 </configfiles>
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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61 <inputs>
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62 <param name="image" type="data" format="ome.tiff" label="Input image in OME-tiff format"/>
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63 <param name="channel_csv" type="data" format="csv" label="Channel Metadata CSV"/>
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64 </inputs>
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65 <outputs>
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66 <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="image" value="rename_test.tiff" />
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71 <param name="channel_csv" value="rename_channels.csv" />
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72 <output name="renamed_image" ftype="ome.tiff">
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73 <assert_contents>
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74 <has_size value="44000" delta="1000" />
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75 </assert_contents>
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76 </output>
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77 <assert_stdout>
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78 <has_text text="Channel 0 renamed to DNA_6" />
18f6be63414c planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 339f5497446066ca76c27460da2eef4f6e0fa36e
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79 <has_text text="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 </assert_stdout>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84 ]]></help>
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85 <expand macro="citations" />
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86 </tool>