<tool id="palom" name="palom" version="2021.12.0.0">
    <description>Piecewise alignment for layers of mosaics. A tool for registering whole-slide images with different IHC stainings</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        
        ln -s "$reference_image" ./ref.svs &&

        ln -s "$channels" ./channels.csv &&

        #for $i in $moving_images:
            ln -s "$i" "${i.name}" &&
        #end for

        python "$script"

    ]]></command>
    <configfiles>
        <configfile name = "script">
import os
import pathlib
import pandas as pd
import palom
from palom.cli.svs import run_palom

cwd = os.getcwd()

ref_img = pathlib.Path(os.path.join(cwd,"ref.svs"))

images = [ref_img]
channels = ["hematoxylin"]
modes = ["hematoxylin"]

#for $i in $moving_images:
img = pathlib.Path("${i.name}")
images.append(img)
#end for

channel_df = pd.read_csv(os.path.join(cwd, "channels.csv"))
channel_df = channel_df.astype({'channel':'string'})
channels += list(channel_df['channel'])
modes += list(channel_df['mode'])

pixel_size = None

#if $pixel_size:
pixel_size = int($pixel_size)
#end if

level = 0

#if $level:
level = int($level)
#end if

output_path = pathlib.Path(os.path.join(cwd, "registered.ome.tiff"))

qc_path = output_path.parent / 'qc'

os.mkdir(qc_path)

run_palom(
    img_paths = images,
    img_modes = modes,
    pixel_size = pixel_size,
    channel_names = channels,
    output_path = output_path,
    qc_path = qc_path,
    level = level
)
        </configfile>
    </configfiles>
    <inputs>
        <param name="reference_image" type="data" format="tiff" label="Hematoxylin reference image" help="An H+E image in .svs format"/>
        <param name="moving_images" type="data_collection" label="Moving Images (data collection)" help="A collection of svs-format images to align to the reference image"/>
        <param name="channels" type="data" label="Channel and mode dataframe" help="A CSV file with 'channel' and 'mode' columns, with a row corresponding to each moving image"/>
        <param name="pixel_size" type="integer" optional="true" label="Pixel Size" help="defaults to px size of reference image"/>
        <param name="level" type="integer" optional="true" label="Level" help="pyramid level, defaults to 0 (lowest level)"/>
    </inputs>
    <outputs>
        <collection name="qc_plots" type="list" label="${tool.name}: qc_plots">
            <discover_datasets pattern="__name_and_ext__" directory="qc" ext="png" visible="false"/>
        </collection>
        <data name="registered" from_work_dir="registered.ome.tiff" format="ome.tiff"/>
    </outputs>
    <help><![CDATA[
# PALOM
registration of whole-slide images with different IHC stainings

Tool github: https://github.com/Yu-AnChen/palom

# Main developer 

Yu-An Chen (https://github.com/Yu-AnChen)
    ]]></help>
    <expand macro="citations" />
</tool>