# HG changeset patch
# User ebi-gxa
# Date 1591362779 14400
# Node ID 232937b5bb8fb86c98a16c11c9e5647b23f5ad0c
# Parent  3bce5710a90b8e9553af7fa866d2a78773e7ab41
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 121972f836fc6f5a60390abcdc1e2fe904b79072"

diff -r 3bce5710a90b -r 232937b5bb8f scanpy-neighbours.xml
--- a/scanpy-neighbours.xml	Thu Mar 12 05:18:41 2020 -0400
+++ b/scanpy-neighbours.xml	Fri Jun 05 09:12:59 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
+<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@">
   <description>to derive kNN graph</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -9,7 +9,11 @@
 ln -s '${input_obj_file}' input.h5 &&
 PYTHONIOENCODING=utf-8 scanpy-neighbors
 #if $settings.default == "false"
-    --n-neighbors '${settings.n_neighbours}'
+    #if $settings.n_neighbors_file
+        --n-neighbors \$( cat $settings.n_neighbors_file )
+    #elif $settings.n_neighbors
+        --n-neighbors '${settings.n_neighbors}'
+    #end if
     --method '${settings.method}'
     --random-state '${settings.random_seed}'
     #if $settings.use_rep != "auto"
@@ -31,14 +35,16 @@
       <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
       <when value="true"/>
       <when value="false">
-        <param name="n_neighbours" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbours used"/>
+        <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">
           <option value="X_pca" selected="true">X_pca, use PCs</option>
           <option value="X">X, use normalised expression values</option>
         </param>
         <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
         <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"
-               label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbours)"/>
+               label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>
         <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
           <option value="umap" selected="true">UMAP</option>
           <option value="gauss">Gaussian</option>
@@ -58,7 +64,7 @@
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
       <param name="default" value="false"/>
-      <param name="n_neighbours" value="15"/>
+      <param name="n_neighbors" value="15"/>
       <param name="n_pcs" value="50"/>
       <param name="knn" value="true"/>
       <param name="random_seed" value="0"/>
diff -r 3bce5710a90b -r 232937b5bb8f scanpy_macros2.xml
--- a/scanpy_macros2.xml	Thu Mar 12 05:18:41 2020 -0400
+++ b/scanpy_macros2.xml	Fri Jun 05 09:12:59 2020 -0400
@@ -64,6 +64,7 @@
 	journal = {GitHub repository},
 	url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
       }</citation>
+      <citation type="doi">10.1101/2020.04.08.032698</citation>
     </citations>
   </xml>