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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 283d7d6ae717a1ebdf389d022126946f52e64529
author bgruening
date Wed, 07 Jan 2026 17:21:47 +0000
parents 130d15e15378
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130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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1 <tool id="cellposesam" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>with Cellpose-SAM</description>
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3 <macros>
1
bc1410a8a247 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 283d7d6ae717a1ebdf389d022126946f52e64529
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4 <token name="@TOOL_VERSION@">4.0.8</token>
0
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">cellpose</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 export MKL_NUM_THREADS=1
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13 && mkdir ./output
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14 && ln -s '${img_in}' './image.${img_in.ext}'
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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15
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16 && cellpose --image_path ./image.${img_in.ext} --no_npy --savedir ./output
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18 #if $save_png
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19 --save_png
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20 #end if
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22 #if $save_tif
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23 --save_tif
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24 #end if
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130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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26 #if $save_flows
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27 --save_flows
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28 #end if
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130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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30 #if $save_outlines
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31 --save_outlines
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32 #end if
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33
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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34 #if $use_gpu
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35 --use_gpu
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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36 #end if
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37
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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38 #if $no_norm
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39 --no_norm
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40 #end if
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41
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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42 #if $diameter
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43 --diameter $diameter
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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44 #end if
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45
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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46 #if $no_resample
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47 --no_resample
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48 #end if
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49
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50 --flow_threshold $flow_threshold
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51 --cellprob_threshold $cellprob_threshold
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52 --niter $niter
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53 --anisotropy $anisotropy
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54
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55 #if $do_3D
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56 --do_3D
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57 #end if
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58
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59 #if $z_axis
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60 --z_axis $z_axis
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61 #end if
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62
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63 #if $channel_axis
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64 --channel_axis $channel_axis
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65 #end if
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66
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67 #if $no_interp
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68 --no_interp
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69 #end if
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70
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71 #if $exclude_on_edges
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72 --exclude_on_edges
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73 #end if
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74
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75 #if $transformer
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76 --transformer
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77 #end if
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78 > ./cp.log 2>&1
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79 ]]>
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80 </command>
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81 <configfiles>
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82 <inputs name="inputs" />
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83 </configfiles>
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84 <inputs>
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85 <param name="img_in" type="data" format="ome.tiff,tiff,jpg,png" label="Choose the image file for segmentation (usually after registration)">
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86 <validator type="dataset_metadata_in_range" metadata_name="frames" min="0" max="1" message="Input image is multi-frame, must be single-frame"/>
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87 </param>
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88 <param name="save_png" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Save masks as png?"/>
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89 <param name="save_tif" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Save masks as tiff?"/>
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90 <param name="save_flows" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Save RGN images of flows when masks are saved?"/>
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91 <param name="save_outlines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Save RGB outline images when masks are saved"/>
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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92 <param name="z_axis" type="integer" optional="true" min="0" label="Z axis" help="The axis of the image which corresponds to the image channels and to the z axis, zero-based." />
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93 <param name="channel_axis" type="integer" optional="true" min="0" label="Channel axis" help="The axis (0-based) of the image which corresponds to the image channels and to the z axis" />
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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94 <param name="use_gpu" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Whether to use GPU?" />
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95 <section name="options" title="Advanced Options" expanded="False">
130d15e15378 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 81c31a317150556704cc02ac5f05eedb0a47e0b2
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96 <param name="no_norm" type="boolean" label="Do not normalize images" truevalue="true" falsevalue="false" checked="false"/>
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97 <param name="diameter" type="float" optional="true" label="Cell or nuclei diameter in pixels" help="Use to resize cells to the training diameter. Leave blank for automated estimation."/>
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98 <param name="no_resample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables flows/cellprob resampling to original image size before computing masks."
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99 help="Using this flag will make more masks more jagged with larger diameter settings."/>
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100 <param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Interpolate when running dynamics."/>
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101 <param name="flow_threshold" type="float" min="0" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/>
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102 <param name="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/>
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103 <param name="niter" type="integer" min="0" value="0" label="Number of iterations"
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104 help="Number of iterations for dynamics for mask creation, default of 0 means it is proportional to diameter, set to a larger number like 2000 for very long ROIs"/>
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105 <param name="anisotropy" type="float" min="0" value="1.0" label="Anisotropy of volume in 3D"
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106 help="By default, sets the number of iterations to be proportional to the ROI diameter. For longer ROIs, more iterations might be needed."/>
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107 <param name="exclude_on_edges" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Discard masks which touch edges of image?" />
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108 <param name="do_3D" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to run 3D segmentation on 4D image input?"/>
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109 <param name="transformer" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use transformer backnone" help="pretrained model from Cellpose3 is transformer_cp3"/>
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110 </section>
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111 <param name="detailed_output" type="boolean" label="Detailed logging file?" help="If set, a CellPose log file will be generated." />
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112 </inputs>
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113 <outputs>
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114 <data format="tiff" name="cp_tiff" from_work_dir="output/image_cp_masks.tif" label="Cellpose SAM masks in TIFF">
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115 <filter>save_tif</filter>
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116 </data>
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117 <data format="png" name="cp_png" from_work_dir="output/image_cp_masks.png" label="Cellpose SAM masks in PNG">
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118 <filter>save_png</filter>
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119 </data>
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120 <data format="tiff" name="cp_flows" from_work_dir="output/image_flows_cp_masks.tif" label="RGB images of flows">
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121 <filter>save_flows</filter>
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122 </data>
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123 <data format="tiff" name="cp_flows_dp" from_work_dir="output/image_dP_cp_masks.tif" label="RGB images of flows(dP)">
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124 <filter>save_flows</filter>
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125 </data>
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126 <data format="png" name="cp_outlines" from_work_dir="output/image_outlines_cp_masks.png" label="RGB outline images">
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127 <filter>save_outlines</filter>
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128 </data>
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129 <data format="txt" name="logs" from_work_dir="cp.log" label="CellPose log">
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130 <filter>detailed_output</filter>
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131 </data>
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132 </outputs>
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133 <tests>
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134 <test expect_num_outputs="2">
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135 <param name="img_in" value="image.png"/>
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136 <param name="save_png" value="true" />
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137 <param name="save_tif" value="true"/>
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138 <output name="cp_tiff" file="image_cp_masks.tiff" compare="image_diff" metric="iou"/>
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139 <output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/>
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140 </test>
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141 <test expect_num_outputs="1">
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142 <param name="img_in" value="image3d.tiff"/>
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143 <param name="save_png" value="false"/>
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144 <param name="save_tif" value="true"/>
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145 <param name="use_gpu" value="true" />
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146 <param name="z_axis" value="0" />
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147 <section name="options">
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148 <param name="do_3D" value="true" />
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149 <param name="no_interp" value="true" />
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150 <param name="niter" value="1"/>
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151 </section>
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152 <output name="cp_tiff" file="image3d_cp_masks.tiff" compare="image_diff"/>
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153 </test>
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154 <test expect_num_outputs="5">
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155 <param name="img_in" value="image.png"/>
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156 <param name="save_png" value="true"/>
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157 <param name="save_tif" value="false"/>
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158 <param name="save_flows" value="true"/>
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159 <param name="save_outlines" value="true" />
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160 <param name="use_gpu" value="true" />
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161 <param name="detailed_output" value="true" />
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162 <output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/>
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163 <output name="cp_flows" file="image_flows_cp_masks.tiff" compare="image_diff" />
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164 <output name="cp_flows_dp" file="image_dP_cp_masks.tiff" compare="image_diff" />
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165 <output name="cp_outlines" file="image_outlines_cp_masks.png" compare="image_diff"/>
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166 <output name="logs" ftype='txt'>
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167 <assert_contents>
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168 <has_text_matching expression="1.15G/1.15G" />
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169 </assert_contents>
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170 </output>
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171 </test>
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172 <test expect_num_outputs="1">
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173 <param name="img_in" value="image.png" />
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174 <param name="save_png" value="true" />
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175 <param name="save_tif" value="false" />
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176 <param name="use_gpu" value="true" />
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177 <section name="options">
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178 <param name="no_norm" value="false" />
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179 <param name="no_resample" value="false" />
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180 <param name="diameter" value="10" />
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181 <param name="flow_threshold" value="0.5" />
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182 <param name="cellprob_threshold" value="0.0" />
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183 <param name="niter" value="10" />
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184 <param name="anisotropy" value="1.0" />
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185 <param name="do_3D" value="false" />
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186 <param name="transformer" value="false" />
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187 </section>
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188 <param name="detailed_output" value="false" />
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189 <output name="cp_png" file="image_cp_masks1.png" compare="image_diff" metric="iou" eps="0.02" />
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190 </test>
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191 </tests>
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192 <help>
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193 <![CDATA[
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194 Cellpose-SAM: superhuman generalization for cellular segmentation
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195 ]]>
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196 </help>
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197 <citations>
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198 <citation type="doi">https://doi.org/10.1101/2025.04.28.651001</citation>
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199 </citations>
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200 </tool>