changeset 12:c78c930e3263 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-neighbours.xml	Fri Jun 05 09:12:59 2020 -0400
+++ b/scanpy-neighbours.xml	Mon Sep 07 14:02:36 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy11" 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>
@@ -15,6 +15,7 @@
         --n-neighbors '${settings.n_neighbors}'
     #end if
     --method '${settings.method}'
+    --metric '${settings.metric}'
     --random-state '${settings.random_seed}'
     #if $settings.use_rep != "auto"
         --use-rep '${settings.use_rep}'
@@ -38,7 +39,7 @@
         <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
         <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
                label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
-        <param name="use_rep" type="text" label="Use the indicated representation">
+        <param name="use_rep" type="select" label="Use the indicated representation">
           <option value="X_pca" selected="true">X_pca, use PCs</option>
           <option value="X">X, use normalised expression values</option>
         </param>
@@ -48,6 +49,32 @@
         <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
           <option value="umap" selected="true">UMAP</option>
           <option value="gauss">Gaussian</option>
+          <option value="rapids">RAPIDS</option>
+        </param>
+        <param name="metric" argument="--metric" type="select" label="A known metric’s name">
+          <option value="euclidean" selected="true">Euclidean</option>
+          <option value="cityblock">cityblock</option>
+          <option value="cosine">cosine</option>
+          <option value="l1">l1</option>
+          <option value="l2">l2</option>
+          <option value="manhattan">manhattan</option>
+          <option value="braycurtis">braycurtis</option>
+          <option value="canberra">canberra</option>
+          <option value="chebyshev">chebyshev</option>
+          <option value="correlation">correlation</option>
+          <option value="dice">dice</option>
+          <option value="hamming">hamming</option>
+          <option value="jaccard">jaccard</option>
+          <option value="kulsinski">kulsinski</option>
+          <option value="mahalanobis">mahalanobis</option>
+          <option value="minkowski">minkowski</option>
+          <option value="rogerstanimoto">rogerstanimoto</option>
+          <option value="russelrao">russelrao</option>
+          <option value="seuclidan">seuclidian</option>
+          <option value="sokalmichener">sokalmichener</option>
+          <option value="sokalsneath">sokalsneath</option>
+          <option value="sqeuclidean">sqeuclidean</option>
+          <option value="yule">yule</option>
         </param>
         <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/>
       </when>

--- a/scanpy_macros2.xml	Fri Jun 05 09:12:59 2020 -0400
+++ b/scanpy_macros2.xml	Mon Sep 07 14:02:36 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>