diff scanpy_macros.xml @ 2:a13cc1d401b7 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ba0c88ab1b077a0b1c60c8d3c529e72ca6946226"

--- a/scanpy_macros.xml	Wed Mar 20 12:00:08 2019 -0400
+++ b/scanpy_macros.xml	Thu Mar 12 09:10:21 2020 +0000
@@ -38,9 +38,14 @@
       <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>
@@ -87,4 +92,18 @@
     <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>