Merge pull request #53 from kostrykin/biohackeu23

applies the new conventions for imaging tools agreed at BioHackEU23
goeckslab · Feb 28, 2024 · 130ef7e · 130ef7e
2 parents 384bcb7 + f1a88b2
commit 130ef7e
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diff --git a/tools/mesmer/mesmer.xml b/tools/mesmer/mesmer.xml
@@ -1,10 +1,14 @@
-<tool id="mesmer" name="Mesmer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
-    <description>Mesmer for whole-cell segmentation of multiplexed tissue imaging data</description>
+<tool id="mesmer" name="Perform segmentation of multiplexed tissue data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+    <description>with Mesmer</description>
 
     <macros>
         <import>macros.xml</import>
     </macros>
 
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 

diff --git a/tools/mti-utils/.shed.yml b/tools/mti-utils/.shed.yml
@@ -1,5 +1,11 @@
 owner: goeckslab
 remote_repository_url: https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils
+homepage_url: https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils
+long_description: |
+    A suite of tool wrapper for Multiplex Tissue Imaging (MTI) utilities.
+    These include simple custom scripts for renaming channels in OME-TIFF metadata, 
+    and singal-processing for tabular intensity data. More utilities may be added in
+    the future. 
 categories:
   - Imaging
 exclude:

diff --git a/tools/mti-utils/macros.xml b/tools/mti-utils/macros.xml
@@ -11,10 +11,11 @@
     </xml>
     <xml name="citations">
         <citations>
+        <citation type="doi">10.1101/2022.08.18.504436</citation>
         </citations>
     </xml>
 
     <token name="@TOOL_VERSION@">0.0.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">19.01</token>
 </macros>
diff --git a/tools/mti-utils/process_intensities.xml b/tools/mti-utils/process_intensities.xml
@@ -1,8 +1,11 @@
 <tool id="cell_intensity_processing" name="Process single-cell intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>Options to correct for exposure time, autofluorescence subtraction, or compute signal-to-background ratio.</description>
+    <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
     <expand macro="requirements" />
     <command detect_errors="aggressive"><![CDATA[
         
@@ -109,8 +112,7 @@ tissue imaging data.
 3. Signal-to-background ratio - Divide single-cell mmean marker intensities by respective AF/bg channel mean intensity specified in channel metadata
 
 **Outputs**
-1. Feature observation matrix with processed intensities for all markers in channel metadata file. 
-   CellIDs, centroids, and morphological data remain unchanged.
+1. Feature observation matrix with processed intensities for all markers in channel metadata file. CellIDs, centroids, and morphological data remain unchanged.
     ]]></help>
     <expand macro="citations" />
-</tool>
+</tool>
diff --git a/tools/mti-utils/rename_tiff_channels.xml b/tools/mti-utils/rename_tiff_channels.xml
@@ -1,11 +1,14 @@
-<tool id="rename_tiff_channels" name="Rename OME-TIFF Channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>Change the channel names in the XML metadata of OME-TIFF images</description>
+<tool id="rename_tiff_channels" name="Rename OME-TIFF channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>with ome-types</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-
+
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+
     <expand macro="requirements"/>
-    <expand macro="version_cmd"/>
 
     <stdio>
         <regex match=".*XMLSyntaxError.*"
@@ -14,6 +17,8 @@
                description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
     </stdio>
 
+    <expand macro="version_cmd"/>
+
     <command detect_errors="aggressive"><![CDATA[
 
         cp '$image' ./renamed_image.ome.tiff && 
@@ -81,6 +86,9 @@ print(tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff')))
         </test>
     </tests>
     <help><![CDATA[
+    Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the 
+    OME XML metadata. CSV file must contain column 'marker_name' which will populate the XML
+    metadata with channel names in the order provided in the CSV file. 
     ]]></help>
     <expand macro="citations" />
 </tool>
diff --git a/tools/squidpy/.shed.yml b/tools/squidpy/.shed.yml
@@ -2,6 +2,11 @@ owner: goeckslab
 homepage_url: https://squidpy.readthedocs.io/en/stable/
 remote_repository_url: https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy
 description: Squidpy is a tool for the analysis and visualization of spatial molecular data.
+long_description: |
+  Squidpy is a tool for the analysis and visualization of spatial molecular data. 
+  It builds on top of scanpy and anndata, from which it inherits modularity and scalability. 
+  It provides analysis tools that leverages the spatial coordinates of the data, 
+  as well as tissue images if available.
 categories:
   - Imaging
   - Proteomics

diff --git a/tools/squidpy/main_macros.xml b/tools/squidpy/main_macros.xml
@@ -1,7 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">1.1.2</token>
     <token name="@PROFILE@">20.01</token>
-    <token name="@VERSION_SUFFIX@">1</token> 
+    <token name="@VERSION_SUFFIX@">2</token> 
 
     <xml name="macro_stdio">
         <stdio>

diff --git a/tools/squidpy/squidpy_spatial.xml b/tools/squidpy/squidpy_spatial.xml
@@ -1,8 +1,11 @@
-<tool id="squidpy_spatial" name="Squidpy Graph and Plotting" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>for spatial analysis </description>
+<tool id="squidpy_spatial" name="Analyze and visualize spatial multi-omics data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>with Squidpy</description>
     <macros>
         <import>main_macros.xml</import>
     </macros>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
     <expand macro="squidpy_requirements"/>
     <expand macro="macro_stdio" />
     <version_command>echo "@TOOL_VERSION@"</version_command>
@@ -257,7 +260,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="anndata" value="imc.h5ad" ftype="h5ad" />
             <param name="selected_tool" value="spatial_neighbors" />
             <output name="output">
@@ -266,7 +269,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
             <param name="selected_tool" value="nhood_enrichment" />
             <param name="cluster_key" value="cell type" />
@@ -277,7 +280,7 @@
             </output>
             <output name="output_plot" file="imc_nhood_enrichment.png" compare="sim_size" delta="2000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
             <param name="selected_tool" value="co_occurrence" />
             <param name="cluster_key" value="cell type" />
@@ -288,7 +291,7 @@
             </output>
             <output name="output_plot" file="imc_co_occurrence.png" compare="sim_size" delta="2000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
             <param name="selected_tool" value="centrality_scores" />
             <param name="cluster_key" value="cell type" />
@@ -299,7 +302,7 @@
             </output>
             <output name="output_plot" file="imc_centrality_scores.png" compare="sim_size" delta="2000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
             <param name="selected_tool" value="interaction_matrix" />
             <param name="cluster_key" value="cell type" />
@@ -310,7 +313,7 @@
             </output>
             <output name="output_plot" file="imc_interaction_matrix.png" compare="sim_size" delta="2000" />
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
             <param name="selected_tool" value="ripley" />
             <param name="cluster_key" value="cell type" />
@@ -341,6 +344,5 @@ This tool includes various of single cell spatial analysis utils provided by Squ
 
         ]]>
     </help>
-    <citations>
-    </citations>
+    <expand macro="citations" />
 </tool>
diff --git a/tools/vitessce/.shed.yml b/tools/vitessce/.shed.yml
@@ -6,9 +6,15 @@ exclude:
   - dependencies
 remote_repository_url: https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce
 homepage_url: https://github.com/vitessce/vitessce
+long_description: |
+    Vitessce enables visual analysis of multi-modal assay types which probe biological systems 
+    through techniques such as microscopy, genomics, and transcriptomics.
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
   description_template: "Wrapper for vitessce tool: {{ tool_name }}"
 suite:
   name: suite_vitessce
   description: Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
+  long_description: |
+      Vitessce enables visual analysis of multi-modal assay types which probe biological systems 
+      through techniques such as microscopy, genomics, and transcriptomics.
diff --git a/tools/vitessce/gate_finder.xml b/tools/vitessce/gate_finder.xml
@@ -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" />

diff --git a/tools/vitessce/main_macros.xml b/tools/vitessce/main_macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.4</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.01</token>
 
     <xml name="vitessce_requirements">
@@ -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
             &&

diff --git a/tools/vitessce/vitessce_spatial.xml b/tools/vitessce/vitessce_spatial.xml
@@ -1,10 +1,14 @@
-<tool id="vitessce_spatial" name="Vitessce Visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>integrative visualization of multi-modal, spatial single-cell data</description>
+<tool id="vitessce_spatial" name="Run multi-modal single-cell visualization" 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> "@VERSION@"</version_command>
@@ -18,10 +22,14 @@
         <param name="image" type="data" format="ome.tiff" label="Select the OME Tiff image" />
         <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
         <conditional name="do_phenotyping">
-            <param name="phenotyping_choice" type="boolean" checked="true" label="Whether to do phenotyping">
+            <param name="phenotyping_choice" type="select" label="Add annotations or visualizations from Anndata file">
+                <option value="no_h5ad" selected="true">Do not add elements from Anndata file</option>
+                <option value="add_h5ad">Add elements from Anndata file</option>
             </param>
-            <when value="true">
-                <param name="anndata" type="data" format="h5ad" label="Select the anndata contaning phenotyping info" />
+            <when value="no_h5ad">
+            </when>
+            <when value="add_h5ad">
+                <param name="anndata" type="data" format="h5ad" label="Select the anndata file" />
                 <conditional name="scatterplot_embeddings">
                     <param name="embedding" type="select" label="Select an embedding algorithm for scatterplot">
                         <option value="umap" selected="true">UMAP</option>
@@ -58,7 +66,7 @@
                     </when>
                 </conditional>
                 <conditional name="phenotype_factory">
-                    <param name="phenotype_mode" type="select" label="Input phenotyping keys">
+                    <param name="phenotype_mode" type="select" label="Input the anndata key to display">
                         <option value="choices" selected="true">Multiple choices</option>
                         <option value="type_in">Type in</option>
                     </param>
@@ -76,8 +84,6 @@
                     </when>
                 </conditional>
             </when>
-            <when value="false">
-            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -87,7 +93,7 @@
         <test>
             <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />
             <conditional name="do_phenotyping">
-                <param name="phenotyping_choice" value="yes" />
+                <param name="phenotyping_choice" value="add_h5ad" />
                 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" />
                 <conditional name="phenotype_factory">
                     <param name="phenotype_mode" value="type_in" />
@@ -99,7 +105,7 @@
         <test>
             <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />
             <conditional name="do_phenotyping">
-                <param name="phenotyping_choice" value="yes" />
+                <param name="phenotyping_choice" value="add_h5ad" />
                 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" />
                 <conditional name="scatterplot_embeddings">
                     <param name="embedding" value="pca" />
@@ -114,7 +120,7 @@
         <test>
             <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />
             <conditional name="do_phenotyping">
-                <param name="phenotyping_choice" value="no" />
+                <param name="phenotyping_choice" value="no_h5ad" />
             </conditional>
             <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />
         </test>