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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
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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1 <tool id="palom" name="palom" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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2 <description>Piecewise alignment for layers of image mosaics.</description>
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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3
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b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
watsocam
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4 <macros>
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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5 <import>macros.xml</import>
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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6 </macros>
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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7
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8 <expand macro="requirements" />
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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9
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10 <command detect_errors="exit_code"><![CDATA[
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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12 ln -s '$reference_image' './ref.svs' &&
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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14 ln -s '$channels' './channels.csv' &&
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b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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16 #for $i in $moving_images:
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17 ln -s '$i' '${i.name}' &&
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18 #end for
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20 python '$script'
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22 ]]></command>
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23 <configfiles>
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24 <configfile name = "script">
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25 import os
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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26 import pathlib
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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27 import pandas as pd
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28 import matplotlib.pyplot as plt
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29 import palom
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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30 from palom.cli.svs import run_palom
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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31
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goeckslab
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32 plt.switch_backend('agg')
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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33
0
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34 cwd = os.getcwd()
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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35
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36 ref_img = pathlib.Path(os.path.join(cwd,'ref.svs'))
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37
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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38 images = [ref_img]
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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39 channels = ['hematoxylin']
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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40 modes = ['hematoxylin']
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41
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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42 #for $i in $moving_images:
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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43 img = pathlib.Path('${i.name}')
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44 images.append(img)
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45 #end for
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46
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e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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47 channel_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
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48 channel_df = channel_df.astype({'channel':'string'})
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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49 channels += list(channel_df['channel'])
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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50 modes += list(channel_df['mode'])
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51
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52 pixel_size = None
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53
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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54 #if $pixel_size:
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55 pixel_size = float($pixel_size)
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56 #end if
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57
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58 level = int($level)
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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59 downscale_factor = int($downscale_factor)
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60
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61 output_path = pathlib.Path(os.path.join(cwd, 'registered.ome.tiff'))
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62
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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63 qc_path = output_path.parent / 'qc'
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64
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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65 os.mkdir(qc_path)
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66
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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67 run_palom(
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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68 img_paths = images,
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69 img_modes = modes,
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70 pixel_size = pixel_size,
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71 channel_names = channels,
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72 output_path = output_path,
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73 qc_path = qc_path,
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74 level = level,
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75 downscale_factor = downscale_factor
0
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76 )
b66b59713319 "planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 84aa6670d94fc7c7ef3178c606896f678119559e"
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77 </configfile>
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78 </configfiles>
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79 <inputs>
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80 <param name="reference_image" type="data" format="tiff" label="Hematoxylin reference image" help=".svs format image to align to"/>
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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81 <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"/>
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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82 <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"/>
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
goeckslab
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83 <param name="pixel_size" type="float" optional="true" label="Pixel size (optional)" help="defaults to px size of reference image"/>
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goeckslab
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84 <param name="level" type="integer" value="0" label="Pyramid level" help="pyramid level, defaults to 0 (lowest level)"/>
e30f622ef2c3 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/palom commit 08d9f2d59c26e67a162d75ae6e8b5fa734ab7b3c
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85 <param name="downscale_factor" type="integer" value="2" label="Pyramid downscale factor" help="Default of 2 makes pyramid downscaling compatible with Avivator and Vitessce"/>
0
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86 </inputs>
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87 <outputs>
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88 <collection name="qc_plots" type="list" label="${tool.name}: qc_plots">
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89 <discover_datasets pattern="__name_and_ext__" directory="qc" ext="png" visible="false"/>
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90 </collection>
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91 <data name="registered" from_work_dir="registered.ome.tiff" format="ome.tiff"/>
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92 </outputs>
2
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93 <tests>
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94 <test>
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95 <param name="reference_image" value="test_ref.svs"/>
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96 <param name="moving_images">
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97 <collection type="list">
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98 <element name="m1" value="test_moving.svs"/>
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99 </collection>
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100 </param>
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101 <param name="channels" value="test_channels.csv"/>
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102 <param name="level" value="1"/>
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103 <output_collection name="qc_plots" type="list">
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104 <element name="01-test_moving.svs" ftype="png">
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105 <assert_contents>
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106 <has_size value="277000" delta="100000" />
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107 </assert_contents>
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108 </element>
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109 </output_collection>
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110 <output name="registered" ftype="ome.tiff">
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111 <assert_contents>
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112 <has_size value="59000000" delta="20000000" />
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113 </assert_contents>
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114 </output>
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115 </test>
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116 </tests>
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117 <help><![CDATA[
2
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118 ------
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119 PALOM
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120 ------
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121 **PALOM** performs registration of whole-slide images with different IHC stainings.
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122 **Inputs**
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123 1.) Reference image for aligning image mosiacs to
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124 2.) A collection of images to be aligned
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125 3.) File describing the channels/targets
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126
2
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127 **Outputs**
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128 1.) Registered image as ome.tiff
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129 2.) Colleciton of QC plots
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130
2
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131 More details on Github: https://github.com/Yu-AnChen/palom
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132
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133 ]]></help>
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134 <expand macro="citations" />
2
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135 </tool>