Mercurial > repos > ebi-gxa > scanpy_plot_embed

changeset 17:9fafbfcdee0d draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"
author ebi-gxa
date Wed, 05 May 2021 12:12:20 +0000
parents 7c601934578b
children 56d22aa6cb3b
files scanpy-plot-embedding.xml scanpy_macros2.xml
diffstat 2 files changed, 17 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/scanpy-plot-embedding.xml	Mon Apr 12 14:44:32 2021 +0000
+++ b/scanpy-plot-embedding.xml	Wed May 05 12:12:20 2021 +0000
@@ -89,6 +89,7 @@
       <param name="input_format" value="anndata"/>
       <param name="basis" value="X_pca"/>
       <param name="color_by" value="louvain"/>
+      <param name="use_raw" value="false"/>
       <output name="output_png" file="plot_embed.png" ftype="png" compare="sim_size"/>
     </test>
   </tests>
--- a/scanpy_macros2.xml	Mon Apr 12 14:44:32 2021 +0000
+++ b/scanpy_macros2.xml	Wed May 05 12:12:20 2021 +0000
@@ -30,6 +30,14 @@
   <token name="@INPUT_OPTS@">
     --input-format '${input_format}' input.h5
   </token>
+  <token name="@SAVE_MATRIX_OPTS@">
+    #if $save_raw
+      --save-raw
+    #end if
+    #if $save_layer
+      --save-layer ${settings.save_layer}
+    #end if
+  </token>
   <token name="@OUTPUT_OPTS@">
 #if str($output_format).startswith('anndata')
     --show-obj stdout --output-format anndata output.h5
@@ -51,7 +59,7 @@
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="0.3.3">scanpy-scripts</requirement>
+      <requirement type="package" version="0.4.0">scanpy-scripts</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -122,6 +130,13 @@
     </data>
   </xml>
 
+  <xml name="save_matrix_params">
+    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
+      label="Save adata to adata.raw before processing?" />
+    <param name="save_layer" argument="--save-layer" type="text" optional="true"
+      label="Save adata.X to the specified layer before processing."/>
+  </xml>  
+
   <xml name="output_plot_params">
     <param name="fig_title" argument="--title" type="text" label="Figure title"/>
     <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>