Mercurial > repos > goeckslab > gate_finder

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
author goeckslab
date Thu, 20 Feb 2025 19:47:28 +0000
parents 8097f9124f87
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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>
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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" />
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11 <version_command>echo "@TOOL_VERSION@"</version_command>
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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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12 <expand macro="vitessce_cmd" tool_id="gate_finder" />
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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>
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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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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>
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31 <outputs>
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32 <data format="html" name="output" />
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33 <data format="json" name="vitessce_config" from_work_dir="config.json" hidden="true" label="Vitessce config file on ${on_string}" />
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34 </outputs>
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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35 <tests>
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36 <test>
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37 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
5f4a4dd06bc9 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
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38 <param name="masks" value="vitessce_mask.tiff" ftype="tiff" />
5f4a4dd06bc9 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
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39 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
5f4a4dd06bc9 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
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40 <param name="marker" value="DNA_1" />
5f4a4dd06bc9 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
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41 <param name="from_gate" value="6" />
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42 <param name="to_gate" value="8" />
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43 <param name="increment" value=".1" />
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44 <output name="vitessce_config">
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45 <assert_contents>
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46 <has_json_property_with_text property="name" text="OMETIFF" />
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47 <has_json_property_with_text property="name" text="MASKS" />
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48 <has_json_property_with_text property="name" text="DNA_1--6.0" />
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49 <has_json_property_with_text property="name" text="DNA_1--7.9" />
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50 </assert_contents>
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51 </output>
0
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52 </test>
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53 </tests>
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54 <help>
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55 <![CDATA[
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56 **What it does**
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57 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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58
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59 **Input**
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60
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61 OME-TIFF image.
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62 Segmentation masks (optional).
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63 AnnData with marker intensities.
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64
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65 **Output**
6df8d6e42152 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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66
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67 An HTML file with Vitessce component.
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68
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69
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70 ]]>
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71 </help>
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72 <citations>
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73 <citation type="doi">10.31219/osf.io/y8thv</citation>
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74 </citations>
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75 </tool>