ebi-gene-expression-group · pinin4fjords · Apr 12, 2021 · Apr 7, 2021 · Apr 7, 2021 · Apr 7, 2021
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
diff --git a/.tt_skip b/.tt_skip
@@ -0,0 +1 @@
+tools/tertiary-analysis/scanpy/scanpy-integrate-mnn.xml
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@+galaxy1" profile="@PROFILE@">
+<tool id="anndata_ops" name="AnnData Operations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>modifies metadata and flags genes</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@+galaxy4" profile="@PROFILE@">
+<tool id="scanpy_find_cluster" name="Scanpy FindCluster" version="@TOOL_VERSION@+galaxy0" 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@+galaxy4" profile="@PROFILE@">
+<tool id="scanpy_find_markers" name="Scanpy FindMarkers" version="@TOOL_VERSION@+galaxy0" 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-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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_integrate_bbknn" name="Scanpy BBKNN" version="@TOOL_VERSION@+galaxy0" 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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" 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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_integrate_harmony" name="Scanpy Harmony" version="@TOOL_VERSION@+galaxy0" 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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_integrate_mnn" name="Scanpy MNN" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>correct batch effects by matching mutual nearest neighbors</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -94,7 +94,7 @@
     <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/>
   </outputs>
 
-  <tests>
+  <!--<tests>
     <test>
       <param name="input_obj_file" value="find_cluster.h5"/>
       <param name="input_format" value="anndata"/>
@@ -108,7 +108,7 @@
       <param name="output_format" value="anndata"/>
       <output name="output_h5" file="mnn_copy.h5" ftype="h5" compare="sim_size"/>
     </test>
-  </tests>
+  </tests>-->
 
   <help><![CDATA[
     .. class:: infomark

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@+galaxy4" profile="@PROFILE@">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>to derive kNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>

diff --git a/tools/tertiary-analysis/scanpy/scanpy-parameter-iterator.xml b/tools/tertiary-analysis/scanpy/scanpy-parameter-iterator.xml
@@ -1,4 +1,4 @@
-<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy3">
+<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy0">
     <description>produce an iteration over a defined parameter</description>
     <macros>
       <import>scanpy_macros.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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>visualise cell trajectories</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -38,12 +38,18 @@ PYTHONIOENCODING=utf-8 scanpy-cli plot paga
         --edge-width-scale ${settings.edge_width}
     #end if
 #end if
+    #if str($output_format).startswith('anndata')
+        --show-obj stdout --output-format anndata --output-obj output.h5
+    #else
+        --show-obj stdout --output-format loom --output-obj output.h5
+    #end if
     @INPUT_OPTS@
     @PLOT_OPTS@
 ]]></command>
 
   <inputs>
     <expand macro="input_object_params"/>
+    <expand macro="output_object_params"/>
     <param name="use_key" argument="--use-key" type="text" value="paga"
            label="The key in `.uns` that contains trajectory information"/>
     <param name="layout" argument="--layout" type="select" label="Layout functions">
@@ -85,14 +91,17 @@ PYTHONIOENCODING=utf-8 scanpy-cli plot paga
   </inputs>
 
   <outputs>
+    <expand macro="output_data_obj" description="Plotted PAGA"/>
     <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: trajectory plot"/>
   </outputs>
 
   <tests>
     <test>
       <param name="input_obj_file" value="paga.h5"/>
       <param name="input_format" value="anndata"/>
+      <param name="output_format" value="anndata"/>
       <param name="type" value="paga_compare"/>
+      <output name="output_h5" file="plotted_paga.h5" ftype="h5" compare="sim_size"/>
       <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/>
     </test>
   </tests>

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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy0" 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-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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_run_pca" name="Scanpy RunPCA" version="@TOOL_VERSION@+galaxy0" 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@+galaxy2" profile="@PROFILE@">
+<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" 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@+galaxy1" profile="@PROFILE@">
+<tool id="scanpy_run_umap" name="Scanpy RunUMAP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>visualise cell clusters using UMAP</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
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.6.0</token>
+  <token name="@TOOL_VERSION@">1.6.1</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
   <token name="@PROFILE@">18.01</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
@@ -49,7 +49,7 @@ EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.3.2">scanpy-scripts</requirement>
+      <requirement type="package" version="0.3.3">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -68,6 +68,7 @@ EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
 	url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
       }</citation>
       <citation type="doi">10.1101/2020.04.08.032698</citation>
+      <citation type="doi">10.1038/s41592-021-01102-w</citation>
     </citations>
   </xml>
 

diff --git a/tools/tertiary-analysis/scanpy/test-data/plotted_paga.h5 b/tools/tertiary-analysis/scanpy/test-data/plotted_paga.h5
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		tools/tertiary-analysis/scanpy/scanpy-integrate-mnn.xml