comparison rename_tiff_channels.xml @ 5:61fd94c7ce42 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43

4:55bc102d7709

    <configfiles>
        <configfile name = "script">
import os
import sys 
import argparse
import pandas as pd
import ome_types
from ome_types.model import channel
from tifffile import tiffcomment

cwd = os.getcwd()

channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))

    for c_idx, channel in enumerate(level.pixels.channels):

        new_name = channels_df.loc[c_idx, 'marker_name']
        channel.name = new_name

        if l_idx == 0:

            print(f"Channel {c_idx} renamed to {new_name}")

    <outputs>
        <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="image" value="rename_test.tiff" />
            <param name="channel_csv" value="rename_channels.csv" />
            <output name="renamed_image" ftype="ome.tiff">
                <assert_contents>
                    <has_size value="44000" delta="1000" />
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Channel 0 renamed to DNA_6" />
                <has_text text="Updated OME-TIFF metadata" />

5:61fd94c7ce42

    <configfiles>
        <configfile name = "script">
import os
import sys 
import argparse
from itertools import cycle
import pandas as pd
import ome_types
from ome_types.model import channel, Color
from tifffile import tiffcomment

# setting default colors to match avivator
colors = [
    (0,0,255,1.0),     # blue
    (0,255,0,1.0),     # green
    (255,0,255,1.0),   # magenta
    (255,255,0,1.0),   # yellow
    (255,127,0,1.0),   # orange
    (0,255,255,1.0),   # cyan
    (255,255,255,1.0), # white
    (255,0,0,1.0)      # red
]

# convert to repeatable object of primitive int colors 
color_cycle = cycle([Color(c).as_int32() for c in colors])

cwd = os.getcwd()

channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))

    for c_idx, channel in enumerate(level.pixels.channels):

        new_name = channels_df.loc[c_idx, 'marker_name']
        channel.name = new_name
        channel.color = next(color_cycle)

        if l_idx == 0:

            print(f"Channel {c_idx} renamed to {new_name}")

    <outputs>
        <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="image" value="rename_test.ome.tiff" />
            <param name="channel_csv" value="rename_channels.csv" />
            <output name="renamed_image" ftype="ome.tiff">
                <assert_contents>
                    <has_size value="899000" delta="50000" />
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Channel 0 renamed to DNA_6" />
                <has_text text="Updated OME-TIFF metadata" />