Mercurial > repos > goeckslab > gate_finder

changeset 1:8097f9124f87 draft

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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 764f6363e2a9
files gate_finder.xml main_macros.xml
diffstat 2 files changed, 9 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/gate_finder.xml	Thu Sep 08 17:22:53 2022 +0000
+++ b/gate_finder.xml	Wed Feb 28 20:53:12 2024 +0000
@@ -1,8 +1,11 @@
-<tool id="gate_finder" name="Gate Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>displays a series of gating outcomes using Vitessce</description>
+<tool id="gate_finder" name="Perform gating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>with Vitessce</description>
     <macros>
         <import>main_macros.xml</import>
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
     <expand macro="vitessce_requirements"/>
     <expand macro="macro_stdio" />
     <version_command>echo "@VERSION@"</version_command>
@@ -14,7 +17,7 @@
         <param name="image" type="data" format="ome.tiff" label="Select the image (OME-TIFF)" />
         <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
         <section name="do_phenotyping" title=" ">
-            <param name="phenotyping_choice" type="hidden" value="true"/>
+            <param name="phenotyping_choice" type="hidden" value="add_h5ad"/>
         </section>
         <param name="phenotyping_choice" type="hidden" value="yes" />
         <param name="anndata" type="data" format="h5ad" label="Select the anndata containing marker intensities" />
--- a/main_macros.xml	Thu Sep 08 17:22:53 2022 +0000
+++ b/main_macros.xml	Wed Feb 28 20:53:12 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.4</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.01</token>
 
     <xml name="vitessce_requirements">
@@ -16,7 +16,7 @@
     </xml>
 
     <xml name="vitessce_cmd" token_tool_id="vitessce_spatial">
-        <command>
+        <command detect_errors="aggressive">
         <![CDATA[
         export BF_MAX_MEM="\${GALAXY_MEMORY_MB}m" &&
         mkdir -p '${output.files_path}/A/0' &&
@@ -70,7 +70,7 @@
             #if $masks
                 --masks '${output.files_path}/A/0/masks01.ome.tiff'
             #end if
-            #if $do_phenotyping.phenotyping_choice
+            #if $do_phenotyping.phenotyping_choice == 'add_h5ad'
             --anndata '$anndata'
             #end if
             &&