Move to scanpy-scripts 1.1.6 bumping all +galaxy (#305)

ebi-gene-expression-group · Oct 13, 2023 · 162313d · 162313d
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diff --git a/tools/tertiary-analysis/scanpy/anndata_operations.xml b/tools/tertiary-analysis/scanpy/anndata_operations.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="anndata_ops" name="AnnData Operations" version="@TOOL_VERSION@+galaxy92" profile="@PROFILE@">
+<tool id="anndata_ops" name="AnnData Operations" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>modifies metadata and flags genes</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-filter-cells.xml b/tools/tertiary-analysis/scanpy/scanpy-filter-cells.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@" >
+<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@" >
   <description>based on counts and numbers of genes expressed</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-filter-genes.xml b/tools/tertiary-analysis/scanpy/scanpy-filter-genes.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>based on counts and numbers of cells expressed</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-find-cluster.xml b/tools/tertiary-analysis/scanpy/scanpy-find-cluster.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>based on community detection on KNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-find-markers.xml b/tools/tertiary-analysis/scanpy/scanpy-find-markers.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy91" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>to find differentially expressed genes between groups</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-find-variable-genes.xml b/tools/tertiary-analysis/scanpy/scanpy-find-variable-genes.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_find_variable_genes" name="Scanpy FindVariableGenes" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>based on normalised dispersion of expression</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-bbknn.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-bbknn.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_bbknn" name="Scanpy BBKNN" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_integrate_bbknn" name="Scanpy BBKNN" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>batch-balanced K-nearest neighbours</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-combat.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>adjust expression for variables that might introduce batch effect</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-harmony.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>adjust principal components for variables that might introduce batch effect</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-integrate-mnn.xml b/tools/tertiary-analysis/scanpy/scanpy-integrate-mnn.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>correct batch effects by matching mutual nearest neighbors</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-multiplet-scrublet-plot.xml b/tools/tertiary-analysis/scanpy/scanpy-multiplet-scrublet-plot.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_plot_scrublet" name="Scanpy Plot Scrublet" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_plot_scrublet" name="Scanpy Plot Scrublet" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>visualise multiplet scoring distribution</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-multiplet-scrublet.xml b/tools/tertiary-analysis/scanpy/scanpy-multiplet-scrublet.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>remove multiplets from annData objects with Scrublet</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-neighbours.xml b/tools/tertiary-analysis/scanpy/scanpy-neighbours.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>to derive kNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-normalise-data.xml b/tools/tertiary-analysis/scanpy/scanpy-normalise-data.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>to make all cells having the same total expression</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-plot-embedding.xml b/tools/tertiary-analysis/scanpy/scanpy-plot-embedding.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>visualise cell embeddings</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-plot-trajectory.xml b/tools/tertiary-analysis/scanpy/scanpy-plot-trajectory.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>visualise cell trajectories</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-read-10x.xml b/tools/tertiary-analysis/scanpy/scanpy-read-10x.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>into hdf5 object handled by scanpy</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-regress-variable.xml b/tools/tertiary-analysis/scanpy/scanpy-regress-variable.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>variables that might introduce batch effect</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-diffmap.xml b/tools/tertiary-analysis/scanpy/scanpy-run-diffmap.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>calculate diffusion components</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-dpt.xml b/tools/tertiary-analysis/scanpy/scanpy-run-dpt.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_dpt" name="Scanpy DPT" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>diffusion pseudotime inference</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-fdg.xml b/tools/tertiary-analysis/scanpy/scanpy-run-fdg.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>visualise cell clusters using force-directed graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-paga.xml b/tools/tertiary-analysis/scanpy/scanpy-run-paga.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>trajectory inference</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-pca.xml b/tools/tertiary-analysis/scanpy/scanpy-run-pca.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>for dimensionality reduction</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-tsne.xml b/tools/tertiary-analysis/scanpy/scanpy-run-tsne.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>visualise cell clusters using tSNE</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-run-umap.xml b/tools/tertiary-analysis/scanpy/scanpy-run-umap.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>visualise cell clusters using UMAP</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-scale-data.xml b/tools/tertiary-analysis/scanpy/scanpy-scale-data.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
+<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
   <description>to make expression variance the same for all genes</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy_macros2.xml b/tools/tertiary-analysis/scanpy/scanpy_macros2.xml
@@ -69,7 +69,7 @@ EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.1.3">scanpy-scripts</requirement>
+      <requirement type="package" version="1.1.6">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>