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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit af71ccb3b89c9735c6f985a3e8ffe22cd14c0e04
author goeckslab
date Thu, 30 May 2024 17:24:31 +0000
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8097f9124f87 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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1 <tool id="gate_finder" name="Perform gating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
8097f9124f87 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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2 <description>with Vitessce</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
8097f9124f87 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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8 </edam_operations>
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9 <expand macro="vitessce_requirements"/>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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10 <expand macro="macro_stdio" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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11 <version_command>echo "@VERSION@"</version_command>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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12 <expand macro="vitessce_cmd" tool_id="gate_finder" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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13 <configfiles>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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14 <inputs name="inputs" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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15 </configfiles>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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16 <inputs>
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17 <param name="image" type="data" format="ome.tiff" label="Select the image (OME-TIFF)" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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18 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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19 <section name="do_phenotyping" title=" ">
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8097f9124f87 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
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20 <param name="phenotyping_choice" type="hidden" value="add_h5ad"/>
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6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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21 </section>
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22 <param name="phenotyping_choice" type="hidden" value="yes" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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23 <param name="anndata" type="data" format="h5ad" label="Select the anndata containing marker intensities" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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24 <param name="marker" type="text" value="" label="Marker for which gate is to be defined" help="E.g.: CD45." />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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25 <param name="from_gate" type="integer" value="6" label="Start value gate of interest" help="Integer. Optional" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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26 <param name="to_gate" type="integer" value="8" label="End value of the gate of interest." help="Integer. Optional" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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27 <param name="increment" type="float" value="0.1" label="Increments between the start and end values" help="Float." />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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28 <param name="x_coordinate" type="text" value="X_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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29 <param name="y_coordinate" type="text" value="Y_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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30 </inputs>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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31 <outputs>
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32 <data format="html" name="output" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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33 </outputs>
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34 <tests>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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35 <test>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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36 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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37 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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38 <param name="marker" value="CD45" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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39 <param name="from_gate" value="5" />
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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40 <param name="to_gate" value="9" />
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41 <param name="increment" value="0.5" />
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42 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />
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43 </test>
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44 </tests>
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45 <help>
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46 <![CDATA[
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47 **What it does**
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48 This tool, built on top of vitessce visualization components, mimics the find_gate function from scimap (https://scimap.xyz/) to do manual gating for single cell quantification data.
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49
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50 **Input**
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51
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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52 OME-TIFF image.
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53 Segmentation masks (optional).
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54 AnnData with marker intensities.
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55
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56 **Output**
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57
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58 An HTML file with Vitessce component.
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59
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61 ]]>
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62 </help>
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63 <citations>
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64 <citation type="doi">10.31219/osf.io/y8thv</citation>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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65 </citations>
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66 </tool>