changeset 11:a1a7650c5cf2 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

--- a/scanpy-run-paga.xml	Fri Jun 05 09:12:40 2020 -0400
+++ b/scanpy-run-paga.xml	Mon Sep 07 14:01:54 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>trajectory inference</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -9,12 +9,15 @@
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-cli paga
     --groups '${groups}'
-#if $use_graph
-    --use-graph '${use_graph}'
+#if $neighbors_key
+    --neighbors-key '${neighbors_key}'
 #end if
 #if $key_added
     --key-added '${key_added}'
 #end if
+#if $use_rna_velocity
+    --use-rna-velocity
+#end if
     @INPUT_OPTS@
     @OUTPUT_OPTS@
 ]]></command>
@@ -24,8 +27,9 @@
     <expand macro="output_object_params"/>
 
     <param name="groups" argument="--groups" type="text" label="Name of the clustering"/>
-    <param name="use_graph" argument="--use-graph" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/>
+    <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/>
     <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated trajectory"/>
+    <param name="use_rna_velocity" type="boolean" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions." help=" Requires that adata.uns contains a directed single-cell graph with key velocity_graph. This feature might be subject to change in the future."/>
   </inputs>
 
   <outputs>
@@ -34,11 +38,11 @@
 
   <tests>
     <test>
-      <param name="input_obj_file" value="compute_graph.h5"/>
+      <param name="input_obj_file" value="find_cluster.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <param name="groups" value="leiden"/>
-      <param name="use_graph" value="neighbors"/>
+      <param name="groups" value="louvain"/>
+      <param name="neighbors_key" value="neighbors"/>
       <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>

--- a/scanpy_macros2.xml	Fri Jun 05 09:12:40 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 14:01:54 2020 +0000
@@ -1,10 +1,13 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.4.3</token>
+  <token name="@TOOL_VERSION@">1.6.0</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[
 **Version history**
 
+1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
+EMBL-EBI https://www.ebi.ac.uk/
+
 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.
 
 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.
@@ -46,7 +49,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.2.10">scanpy-scripts</requirement>
+      <requirement type="package" version="0.3.0">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>