Mercurial > repos > watsocam > palom
changeset 2:e30f622ef2c3 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
| author | goeckslab |
|---|---|
| date | Tue, 06 Sep 2022 21:15:56 +0000 |
| parents | 69f8e01b2e17 |
| children | |
| files | Dockerfile macros.xml palom_svs.xml test-data/test_channels.csv test-data/test_moving.svs test-data/test_ref.svs |
| diffstat | 6 files changed, 90 insertions(+), 31 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Dockerfile Tue Sep 06 21:15:56 2022 +0000 @@ -0,0 +1,18 @@ +FROM python:3.7.12 + +ENV OPS_VERSION=3.4.1 + +ENV PALOM_VERSION=2022.8.2 + +RUN apt update -y && apt install -y openslide-tools python3-opencv + +RUN cd /opt && \ + wget https://github.com/openslide/openslide/releases/download/v$OPS_VERSION/openslide-$OPS_VERSION.tar.gz && \ + tar -zxvf openslide-$OPS_VERSION.tar.gz && \ + cd openslide-$OPS_VERSION + +RUN /opt/openslide-$OPS_VERSION/configure && \ + make && \ + make install + +RUN pip install zarr==2.10.3 pandas palom==$PALOM_VERSION \ No newline at end of file
--- a/macros.xml Wed May 18 22:55:21 2022 +0000 +++ b/macros.xml Tue Sep 06 21:15:56 2022 +0000 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <container type="docker">quay.io/goeckslab/palom:2021.12.0</container> + <container type="docker">quay.io/goeckslab/palom:@TOOL_VERSION@</container> </requirements> </xml> <xml name="citations"> @@ -9,4 +9,7 @@ <yield /> </citations> </xml> -</macros> \ No newline at end of file + <token name="@TOOL_VERSION@">2022.8.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> +</macros>
--- a/palom_svs.xml Wed May 18 22:55:21 2022 +0000 +++ b/palom_svs.xml Tue Sep 06 21:15:56 2022 +0000 @@ -1,20 +1,23 @@ -<tool id="palom" name="palom" version="2021.12.0.1"> - <description>Piecewise alignment for layers of mosaics. A tool for registering whole-slide images with different IHC stainings</description> +<tool id="palom" name="palom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Piecewise alignment for layers of image mosaics.</description> + <macros> <import>macros.xml</import> </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ - ln -s "$reference_image" ./ref.svs && + ln -s '$reference_image' './ref.svs' && - ln -s "$channels" ./channels.csv && + ln -s '$channels' './channels.csv' && #for $i in $moving_images: - ln -s "$i" "${i.name}" && + ln -s '$i' '${i.name}' && #end for - python "$script" + python '$script' ]]></command> <configfiles> @@ -22,23 +25,26 @@ import os import pathlib import pandas as pd +import matplotlib.pyplot as plt import palom from palom.cli.svs import run_palom +plt.switch_backend('agg') + cwd = os.getcwd() -ref_img = pathlib.Path(os.path.join(cwd,"ref.svs")) +ref_img = pathlib.Path(os.path.join(cwd,'ref.svs')) images = [ref_img] -channels = ["hematoxylin"] -modes = ["hematoxylin"] +channels = ['hematoxylin'] +modes = ['hematoxylin'] #for $i in $moving_images: -img = pathlib.Path("${i.name}") +img = pathlib.Path('${i.name}') images.append(img) #end for -channel_df = pd.read_csv(os.path.join(cwd, "channels.csv")) +channel_df = pd.read_csv(os.path.join(cwd, 'channels.csv')) channel_df = channel_df.astype({'channel':'string'}) channels += list(channel_df['channel']) modes += list(channel_df['mode']) @@ -49,13 +55,10 @@ pixel_size = float($pixel_size) #end if -level = 0 +level = int($level) +downscale_factor = int($downscale_factor) -#if $level: -level = int($level) -#end if - -output_path = pathlib.Path(os.path.join(cwd, "registered.ome.tiff")) +output_path = pathlib.Path(os.path.join(cwd, 'registered.ome.tiff')) qc_path = output_path.parent / 'qc' @@ -68,16 +71,18 @@ channel_names = channels, output_path = output_path, qc_path = qc_path, - level = level + level = level, + downscale_factor = downscale_factor ) </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="float" 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)"/> + <param name="reference_image" type="data" format="tiff" label="Hematoxylin reference image" help=".svs format image to align to"/> + <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 for each moving image"/> + <param name="pixel_size" type="float" optional="true" label="Pixel size (optional)" help="defaults to px size of reference image"/> + <param name="level" type="integer" value="0" label="Pyramid level" help="pyramid level, defaults to 0 (lowest level)"/> + <param name="downscale_factor" type="integer" value="2" label="Pyramid downscale factor" help="Default of 2 makes pyramid downscaling compatible with Avivator and Vitessce"/> </inputs> <outputs> <collection name="qc_plots" type="list" label="${tool.name}: qc_plots"> @@ -85,15 +90,46 @@ </collection> <data name="registered" from_work_dir="registered.ome.tiff" format="ome.tiff"/> </outputs> + <tests> + <test> + <param name="reference_image" value="test_ref.svs"/> + <param name="moving_images"> + <collection type="list"> + <element name="m1" value="test_moving.svs"/> + </collection> + </param> + <param name="channels" value="test_channels.csv"/> + <param name="level" value="1"/> + <output_collection name="qc_plots" type="list"> + <element name="01-test_moving.svs" ftype="png"> + <assert_contents> + <has_size value="277000" delta="100000" /> + </assert_contents> + </element> + </output_collection> + <output name="registered" ftype="ome.tiff"> + <assert_contents> + <has_size value="59000000" delta="20000000" /> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ -# PALOM -registration of whole-slide images with different IHC stainings +------ +PALOM +------ +**PALOM** performs registration of whole-slide images with different IHC stainings. +**Inputs** +1.) Reference image for aligning image mosiacs to +2.) A collection of images to be aligned +3.) File describing the channels/targets -Tool github: https://github.com/Yu-AnChen/palom +**Outputs** +1.) Registered image as ome.tiff +2.) Colleciton of QC plots -# Main developer +More details on Github: https://github.com/Yu-AnChen/palom -Yu-An Chen (https://github.com/Yu-AnChen) ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool>