Mercurial > repos > goeckslab > gate_finder

comparison gate_finder.xml @ 1:8097f9124f87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 130ef7e8ae6cab35866b72617e53d35acc11475a
author goeckslab
date Wed, 28 Feb 2024 20:53:12 +0000
parents 6df8d6e42152
children
comparison
equal deleted inserted replaced
0:6df8d6e42152 1:8097f9124f87
1 <tool id="gate_finder" name="Gate Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="gate_finder" name="Perform gating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>displays a series of gating outcomes using Vitessce</description> 2 <description>with Vitessce</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 </macros> 5 </macros>
6 <edam_operations>
7 <edam_operation>operation_3443</edam_operation>
8 </edam_operations>
6 <expand macro="vitessce_requirements"/> 9 <expand macro="vitessce_requirements"/>
7 <expand macro="macro_stdio" /> 10 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command> 11 <version_command>echo "@VERSION@"</version_command>
9 <expand macro="vitessce_cmd" tool_id="gate_finder" /> 12 <expand macro="vitessce_cmd" tool_id="gate_finder" />
10 <configfiles> 13 <configfiles>
12 </configfiles> 15 </configfiles>
13 <inputs> 16 <inputs>
14 <param name="image" type="data" format="ome.tiff" label="Select the image (OME-TIFF)" /> 17 <param name="image" type="data" format="ome.tiff" label="Select the image (OME-TIFF)" />
15 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" /> 18 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
16 <section name="do_phenotyping" title=" "> 19 <section name="do_phenotyping" title=" ">
17 <param name="phenotyping_choice" type="hidden" value="true"/> 20 <param name="phenotyping_choice" type="hidden" value="add_h5ad"/>
18 </section> 21 </section>
19 <param name="phenotyping_choice" type="hidden" value="yes" /> 22 <param name="phenotyping_choice" type="hidden" value="yes" />
20 <param name="anndata" type="data" format="h5ad" label="Select the anndata containing marker intensities" /> 23 <param name="anndata" type="data" format="h5ad" label="Select the anndata containing marker intensities" />
21 <param name="marker" type="text" value="" label="Marker for which gate is to be defined" help="E.g.: CD45." /> 24 <param name="marker" type="text" value="" label="Marker for which gate is to be defined" help="E.g.: CD45." />
22 <param name="from_gate" type="integer" value="6" label="Start value gate of interest" help="Integer. Optional" /> 25 <param name="from_gate" type="integer" value="6" label="Start value gate of interest" help="Integer. Optional" />