# HG changeset patch
# User ebi-gxa
# Date 1587741793 14400
# Node ID 5036928f60bcff940354cb1cde78f673514c76a2
# Parent  8ee96cde3643da6e77532fb07d83438d71494511
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 8ee96cde3643 -r 5036928f60bc garnett_macros.xml
--- a/garnett_macros.xml	Wed Apr 08 06:32:25 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:23:13 2020 -0400
@@ -4,7 +4,7 @@
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.3">garnett-cli</requirement>
+            <requirement type="package" version="0.0.5">garnett-cli</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -21,7 +21,7 @@
         <citations>
             <citation type="bibtex">
                 @article{,
-                url = {https://doi.org/10.1038/s41592-019-0535-3},           
+                url = {https://doi.org/10.1038/s41592-019-0535-3},
                 author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell},
                 title = {Supervised classification enables rapid annotation of cell atlases},
                 journal = {Nature Methods}
@@ -38,7 +38,7 @@
                   }
             </citation>
             <yield />
+            <citation type="doi">10.1101/2020.04.08.032698</citation>
         </citations>
     </xml>
 </macros>
-
diff -r 8ee96cde3643 -r 5036928f60bc update_marker_file.xml
--- a/update_marker_file.xml	Wed Apr 08 06:32:25 2020 -0400
+++ b/update_marker_file.xml	Fri Apr 24 11:23:13 2020 -0400
@@ -5,7 +5,17 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}' --summary-col '${summary_col}' --cell-type-col '${cell_type_col}' --gene-id-col '${gene_id_col}' --updated-marker-file '${updated_marker_file}' 
+        update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}'    --updated-marker-file '${updated_marker_file}'
+
+        #if $summary_col
+        --summary-col '${summary_col}'
+        #end if
+        #if $cell_type_col
+        --cell-type-col '${cell_type_col}'
+        #end if
+        #if $gene_id_col
+        --gene-id-col '${gene_id_col}'
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="marker_list_obj" label="Marker list object" format="rdata" help="Serialised object containing markers list produced by garnett_transform_markers" />