# HG changeset patch
# User ebi-gxa
# Date 1709052128 0
# Node ID 2f9517a24c7363e6e43b3281d86cbf34c31e3008
# Parent  fadc4fbf8025c6596f5cba31cd7f33d710dc9c1a
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty

diff -r fadc4fbf8025 -r 2f9517a24c73 scanpy-multiplet-scrublet.xml
--- a/scanpy-multiplet-scrublet.xml	Fri Oct 13 14:08:16 2023 +0000
+++ b/scanpy-multiplet-scrublet.xml	Tue Feb 27 16:42:08 2024 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
+<tool id="scanpy_multiplet_scrublet" name="Scanpy Scrublet" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
   <description>remove multiplets from annData objects with Scrublet</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -7,7 +7,7 @@
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${input_obj_file}' input.h5 &&
-PYTHONIOENCODING=utf-8 scanpy-multiplet scrublet 
+PYTHONIOENCODING=utf-8 scanpy-cli multiplet scrublet 
 #if $threshold
     --threshold '${threshold}'
 #end if
@@ -103,7 +103,7 @@
       <param name="input_obj_file" value="read_10x.h5"/>
       <param name="input_format" value="anndata"/>
       <param name="output_format" value="anndata"/>
-      <output name="output_h5" file="scrublet.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" file="scrublet.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
     </test>
   </tests>
 
@@ -114,7 +114,7 @@
 
     Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet(). 
 
-    This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/docsearch/external/scanpy.external.pp.scrublet.html.
+    This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scrublet.html.
 
     **Note**
 
diff -r fadc4fbf8025 -r 2f9517a24c73 scanpy_macros.xml
--- a/scanpy_macros.xml	Fri Oct 13 14:08:16 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-<macros>
-  <token name="@TOOL_VERSION@">1.3.2</token>
-  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
-  <token name="@PLOT_OPTS@">
-#if $do_plotting.plot
-                  -P output.png
-                  --projectio $do_plotting.projection
-                  --components $do_plotting.components
-    #if $do_plotting.color_by
-                  --color-by $do_plotting.color_by
-    #end if
-    #if $do_plotting.groups
-                  --group $do_plotting.groups
-    #end if
-    #if $do_plotting.use_raw
-                  --use-raw
-    #end if
-    #if $do_plotting.palette
-                  --palette $do_plotting.palette
-    #end if
-    #if $do_plotting.edges
-                  --edges
-    #end if
-    #if $do_plotting.arrows
-                  --arrows
-    #end if
-    #if not $do_plotting.sort_order
-                  --no-sort-order
-    #end if
-    #if $do_plotting.frameoff
-                  --frameoff
-    #end if
-#end if
-  </token>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
-      <yield/>
-    </requirements>
-  </xml>
-  <token name="@EXPORT_MTX_OPTS@">
-      ${export_mtx}
-  </token>
-  <token name="@VERSION_HISTORY@"><![CDATA[
-**Version history**
-
-1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.
-
-1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
-EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
-    ]]></token>
-  <xml name="citations">
-    <citations>
-      <citation type="doi">10.1186/s13059-017-1382-0</citation>
-      <citation type="bibtex">
-	@misc{githubscanpy-scripts,
-	author = {Ni Huang, EBI Gene Expression Team},
-	year = {2018},
-	title = {Scanpy-scripts: command line interface for Scanpy},
-	publisher = {GitHub},
-	journal = {GitHub repository},
-	url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
-      }</citation>
-      <yield />
-    </citations>
-  </xml>
-  <xml name="input_object_params">
-    <param name="input_obj_file" argument="--input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
-    <param name="input_format" argument="--input-format" type="select" label="Format of input object">
-      <option value="anndata" selected="true">AnnData format hdf5</option>
-      <option value="loom">Loom format hdf5, current support is incomplete</option>
-    </param>
-  </xml>
-  <xml name="output_object_params">
-    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
-      <option value="anndata" selected="true">AnnData format hdf5</option>
-      <option value="loom">Loom format hdf5, current support is defective</option>
-    </param>
-  </xml>
-  <xml name="output_plot_params">
-    <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
-    <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
-    <param name="projection" argument="--projection" type="select" label="Plot projection">
-      <option value="2d" selected="true">2D</option>
-      <option value="3d">3D</option>
-    </param>
-    <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
-    <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
-    <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
-    <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
-    <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
-    <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
-    <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
-  </xml>
-  <xml name="export_mtx_params">
-    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
-  </xml>
-  <xml name="export_mtx_outputs">
-    <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
-      <filter>export_mtx</filter>
-    </data>
-    <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
-      <filter>export_mtx</filter>
-    </data>
-    <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
-      <filter>export_mtx</filter>
-    </data>
-  </xml>
-</macros>
diff -r fadc4fbf8025 -r 2f9517a24c73 scanpy_macros2.xml
--- a/scanpy_macros2.xml	Fri Oct 13 14:08:16 2023 +0000
+++ b/scanpy_macros2.xml	Tue Feb 27 16:42:08 2024 +0000
@@ -1,9 +1,11 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.8.1</token>
+  <token name="@TOOL_VERSION@">1.9.3</token>
   <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
-  <token name="@PROFILE@">18.01</token>
+  <token name="@PROFILE@">20.09</token>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+1.9.301+galaxy0: Moves to Scanpy 1.9.3
+
 1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
 adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.
 
@@ -69,14 +71,18 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.1.6">scanpy-scripts</requirement>
+        <requirement type="package" version="1.9.301">scanpy-scripts</requirement>
       <yield/>
+      <!-- use this format when you want to test against provisional conda artifacts
+        <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.301  pyhdfd78af_0</container> 
+      -->
     </requirements>
   </xml>
 
   <xml name="citations">
     <citations>
       <yield />
+      <citation type="doi">10.1038/s41592-021-01102-w</citation>
       <citation type="doi">10.1186/s13059-017-1382-0</citation>
       <citation type="bibtex">
 	@misc{githubscanpy-scripts,
@@ -88,7 +94,6 @@
 	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>