# HG changeset patch
# User ebi-gxa
# Date 1587741726 14400
# Node ID ad647e1d14dcdff634f7719e1e9f158f7c75daa3
# Parent  67e6c4455bb8579072b9225591b264f7efc9a830
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 67e6c4455bb8 -r ad647e1d14dc garnett_classify_cells.xml
--- a/garnett_classify_cells.xml	Wed Apr 08 06:22:12 2020 -0400
+++ b/garnett_classify_cells.xml	Fri Apr 24 11:22:06 2020 -0400
@@ -5,7 +5,17 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --cluster-extend '${cluster_extend}' --rank-prob-ratio '${rank_prob_ratio}' --cds-output-obj '${cds_output_obj}'
+        garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-output-obj '${cds_output_obj}'
+
+        #if $cds_gene_id_type
+        --cds-gene-id-type '${cds_gene_id_type}'
+        #end if
+        #if $cluster_extend
+        --cluster-extend '${cluster_extend}'
+        #end if
+        #if $rank_prob_ratio
+        --rank-prob-ratio '${rank_prob_ratio}'
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
diff -r 67e6c4455bb8 -r ad647e1d14dc garnett_macros.xml
--- a/garnett_macros.xml	Wed Apr 08 06:22:12 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:22:06 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>
-