# HG changeset patch
# User ebi-gxa
# Date 1587741777 14400
# Node ID a16b409dee64ae2927c19c96445af84c0f7d444d
# Parent  29117f5b2cd9c5266d75cdd209c82b99a506ddad
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 29117f5b2cd9 -r a16b409dee64 garnett_get_feature_genes.xml
--- a/garnett_get_feature_genes.xml	Wed Apr 08 06:29:13 2020 -0400
+++ b/garnett_get_feature_genes.xml	Fri Apr 24 11:22:57 2020 -0400
@@ -5,7 +5,14 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        garnett_get_feature_genes.R --classifier-object '${classifier_object}' --node '${node}' --database '${database}' --convert-ids '${convert_ids}' --output-path '${output_path}'
+        garnett_get_feature_genes.R --classifier-object '${classifier_object}'  --database '${database}' --output-path '${output_path}'
+
+        #if $node
+        --node '${node}'
+        #end if
+        #if $convert_ids
+        --convert-ids '${convert_ids}'
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="classifier_object" label="classifier object" format="rdata" help="Path to the object of class garnett_classifier, which is either trained via garnett_train_classifier.R or obtained elsewhere" />
diff -r 29117f5b2cd9 -r a16b409dee64 garnett_macros.xml
--- a/garnett_macros.xml	Wed Apr 08 06:29:13 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:22:57 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>
-