Mercurial > repos > perssond > s3segmenter

comparison s3segmenter.xml @ 1:41e8efe8df43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ohsu-comp-bio/S3segmenter commit c8f72e04db2cc6cc26f0359d5aa3b1a972bc6d53"
author watsocam
date Fri, 11 Mar 2022 23:37:49 +0000
parents 37acf42a824b
children 96d0d969ebc9
comparison
equal deleted inserted replaced
0:37acf42a824b 1:41e8efe8df43
1 <tool id="s3segmenter" name="s3segmenter" version="@VERSION@.3" profile="17.09"> 1 <tool id="s3segmenter" name="s3segmenter" version="@VERSION@.0" profile="17.09">
2 <description>S3segmenter is a Python-based set of functions that generates single cell (nuclei and cytoplasm) label masks.</description> 2 <description>S3segmenter is a Python-based set of functions that generates single cell (nuclei and cytoplasm) label masks.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
37 37
38 #if $stackProbPath 38 #if $stackProbPath
39 --stackProbPath ./Probabilities.tif 39 --stackProbPath ./Probabilities.tif
40 #end if 40 #end if
41 41
42 --mask $mask
43 --probMapChan $probMapChan 42 --probMapChan $probMapChan
44 --crop $crop 43 --crop $crop_select.crop
44
45 #if $crop_select.crop == "dearray"
46 --maskPath $crop_select.maskPath
47 #end if
48
45 --cytoMethod $cytoMethod 49 --cytoMethod $cytoMethod
46 --nucleiFilter $nucleiFilter 50 --nucleiFilter $nucleiFilter
47 --nucleiRegion $nucleiRegion 51 --nucleiRegion $nucleiRegion_select.nucleiRegion
52
53 #if $nucleiRegion_select.nucleiRegion == "pixellevel"
54 --pixelThreshold $nucleiRegion_select.pixelThreshold
55 --pixelMaskChan $nucleiRegion_select.pixelMaskChan
56 #end if
57
48 --segmentCytoplasm $segmentCytoplasm 58 --segmentCytoplasm $segmentCytoplasm
49 --cytoDilation $adv.cytoDilation 59 --cytoDilation $adv.cytoDilation
50 --logSigma $adv.logSigma 60 --logSigma $adv.logSigma
51 --CytoMaskChan $adv.CytoMaskChan 61 --CytoMaskChan $adv.CytoMaskChan
52 ##--TissueMaskChan $adv.TissueMaskChan 62 ##--TissueMaskChan $adv.TissueMaskChan
70 80
71 <param name="imagePath" type="data" format="tiff" label="Image File"/> 81 <param name="imagePath" type="data" format="tiff" label="Image File"/>
72 <param name="contoursClassProbPath" type="data" format="tiff" optional="true" label="Contours Class Probabilities"/> 82 <param name="contoursClassProbPath" type="data" format="tiff" optional="true" label="Contours Class Probabilities"/>
73 <param name="nucleiClassProbPath" type="data" format="tiff" optional="true" label="Nuclei Class Probabilities"/> 83 <param name="nucleiClassProbPath" type="data" format="tiff" optional="true" label="Nuclei Class Probabilities"/>
74 <param name="stackProbPath" type="data" format="tiff" optional="true" label="Stack Probabilities"/> 84 <param name="stackProbPath" type="data" format="tiff" optional="true" label="Stack Probabilities"/>
75 <param name="mask" type="select" label="Choose mask: TMA, tissue, none.">
76 <option selected="true" value="tissue">tissue</option>
77 <option value="TMA">TMA</option>
78 <option value="none">none</option>
79 </param>
80 <param name="probMapChan" type="integer" value="-1" label="Probability Maps Channel"/> 85 <param name="probMapChan" type="integer" value="-1" label="Probability Maps Channel"/>
81 <param name="crop" type="select" label="Crop Strategy"> 86
82 <option selected="true" value="noCrop">No Crop</option> 87 <conditional name="crop_select">
83 <option value="autoCrop">Automatic Crop</option> 88 <param name="crop" type="select" label="Crop Strategy">
84 <option value="dearray">De-array</option> 89 <option selected="true" value="noCrop">No Crop</option>
85 <option value="plate">Plate</option> 90 <option value="autoCrop">Automatic Crop</option>
86 </param> 91 <option value="dearray">De-array</option>
92 <option value="plate">Plate</option>
93 </param>
94 <when value="dearray">
95 <param name="maskPath" type="data" format="tiff" label="TMA Mask File"/>
96 </when>
97 </conditional>
98
87 <param name="cytoMethod" type="select" label="Cyto Method"> 99 <param name="cytoMethod" type="select" label="Cyto Method">
88 <option value="hybrid">Hybrid</option> 100 <option value="hybrid">Hybrid</option>
89 <option selected="true" value="distanceTransform">Distance Transform</option> 101 <option selected="true" value="distanceTransform">Distance Transform</option>
90 <option value="bwdistanceTransform">BW Distance Transform</option> 102 <option value="bwdistanceTransform">BW Distance Transform</option>
91 <option value="ring">Ring</option> 103 <option value="ring">Ring</option>
94 <option selected="true" value="IntPM">IntPM</option> 106 <option selected="true" value="IntPM">IntPM</option>
95 <option value="LoG">LoG</option> 107 <option value="LoG">LoG</option>
96 <option value="Int">Int</option> 108 <option value="Int">Int</option>
97 <option value="none">none</option> 109 <option value="none">none</option>
98 </param> 110 </param>
99 <param name="nucleiRegion" type="select" label="Nuclei Region"> 111
100 <option value="watershedContourDist">watershedContourDist</option> 112 <conditional name="nucleiRegion_select">
101 <option selected="true" value="watershedContourInt">watershedContourInt</option> 113 <param name="nucleiRegion" type="select" label="Nuclei Region">
102 <option value="watershedBWDist">watershedBWDist</option> 114 <option value="watershedContourDist">watershedContourDist</option>
103 <option value="dilation">dilation</option> 115 <option selected="true" value="watershedContourInt">watershedContourInt</option>
104 <option value="localThreshold">localThreshold</option> 116 <option value="watershedBWDist">watershedBWDist</option>
105 </param> 117 <option value="dilation">dilation</option>
118 <option value="localThreshold">localThreshold</option>
119 <option value="localMax">localMax</option>
120 <option value="bypass">bypass</option>
121 <option value="pixellevel">pixellevel</option>
122 </param>
123 <when value="pixellevel">
124 <param name="pixelThreshold" type="float" value="-1.0" Label="Pixel Threshold"/>
125 <param name="pixelMaskChan" type="text" value="2" Label="Pixel Mask Channel"/>
126 </when>
127 </conditional>
128
106 <param name="segmentCytoplasm" type="select" label="Segment Cytoplasm"> 129 <param name="segmentCytoplasm" type="select" label="Segment Cytoplasm">
107 <option value="segmentCytoplasm">segmentCytoplasm</option> 130 <option value="segmentCytoplasm">segmentCytoplasm</option>
108 <option selected="true" value="ignoreCytoplasm">ignoreCytoplasm</option> 131 <option selected="true" value="ignoreCytoplasm">ignoreCytoplasm</option>
109 </param> 132 </param>
110 <param name="saveMask" type="boolean" checked="true" label="Save Mask"/> 133 <param name="saveMask" type="boolean" checked="true" label="Save Mask"/>
111 <param name="saveFig" type="boolean" checked="true" label="Save Figure"/> 134 <param name="saveFig" type="boolean" checked="true" label="Save Figure"/>
112 135
113 <section name="adv" title="Advanced Options" expanded="false"> 136 <section name="adv" title="Advanced Options" expanded="false">
114 <param name="cytoDilation" type="integer" value="5" label="Cyto Dilation"/> 137 <param name="cytoDilation" type="integer" value="5" label="Cyto Dilation"/>
115 <param name="logSigma" type="text" value="3 60" label="logSigma"/> 138 <param name="logSigma" type="text" value="3 60" label="logSigma"/>
116 <param name="CytoMaskChan" type="text" value="1" label="Cyto Mask Channel"/> 139 <param name="CytoMaskChan" type="text" value="2" label="Cyto Mask Channel"/>
117 <!-- Bug with S3Segmenter code, expects int not list 140 <!-- Bug with S3Segmenter code, expects int not list
118 <param name="TissueMaskChan" type="text" value="-1" label="Tissue Mask Channel"/> 141 <param name="TissueMaskChan" type="text" value="-1" label="Tissue Mask Channel"/>
119 --> 142 -->
120 <param name="detectPuncta" type="text" value="-1" label="Detect Puncta"/> 143 <param name="detectPuncta" type="text" value="-1" label="Detect Puncta"/>
121 <param name="punctaSigma" type="text" value="1" label="Puncta Sigma"/> 144 <param name="punctaSigma" type="text" value="1" label="Puncta Sigma"/>
123 </section> 146 </section>
124 147
125 148
126 </inputs> 149 </inputs>
127 <outputs> 150 <outputs>
128 <data format="tiff" name="cell_mask" from_work_dir="*/cellMask.tif" label="cellMasks"> 151 <data format="tiff" name="cell_mask" from_work_dir="image/cell.ome.tif" label="cellMasks">
129 <filter>saveMask is True</filter> 152 <filter>saveMask is True</filter>
130 </data> 153 </data>
131 <data format="tiff" name="nuclei_mask" from_work_dir="*/nucleiMask.tif" label="nucleiMasks"> 154 <data format="tiff" name="nuclei_mask" from_work_dir="image/nuclei.ome.tif" label="nucleiMasks">
132 <filter>saveMask is True</filter> 155 <filter>saveMask is True</filter>
133 </data> 156 </data>
134 <data format="tiff" name="cell_outlines" from_work_dir="*/cellOutlines.tif" label="cellOutlines"> 157 <data format="tiff" name="cell_outlines" from_work_dir="image/qc/cellOutlines.ome.tif" label="cellOutlines">
135 <filter>saveFig is True</filter> 158 <filter>saveFig is True</filter>
136 </data> 159 </data>
137 <data format="tiff" name="nuclei_outlines" from_work_dir="*/nucleiOutlines.tif" label="nucleiOutlines"> 160 <data format="tiff" name="nuclei_outlines" from_work_dir="image/qc/nucleiOutlines.ome.tif" label="nucleiOutlines">
138 <filter>saveFig is True</filter> 161 <filter>saveFig is True</filter>
139 </data> 162 </data>
140 </outputs> 163 </outputs>
141 <help><![CDATA[ 164 <help><![CDATA[
142 Inputs are: 165 Inputs are: