changeset 17:2fe4b4cba312 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"

--- a/scanpy-plot-trajectory.xml	Tue Mar 23 18:13:46 2021 +0000
+++ b/scanpy-plot-trajectory.xml	Mon Apr 12 14:44:49 2021 +0000
@@ -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 @@
         --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">
@@ -85,6 +91,7 @@
   </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>
 
@@ -92,7 +99,9 @@
     <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>

--- a/scanpy_macros2.xml	Tue Mar 23 18:13:46 2021 +0000
+++ b/scanpy_macros2.xml	Mon Apr 12 14:44:49 2021 +0000
@@ -1,10 +1,12 @@
 <macros>
-  <token name="@TOOL_VERSION@">1.6.0</token>
+  <token name="@TOOL_VERSION@">1.7.2</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**
 
+1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.
+
 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/
 
@@ -49,7 +51,7 @@
 
   <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 +70,7 @@
 	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>