# HG changeset patch
# User ebi-gxa
# Date 1587741700 14400
# Node ID 211241c50ccf9078b646af0737ea62cf64b92269
# Parent  2142ecf6ff022365a35f02f78f931b4b13ad420e
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 2142ecf6ff02 -r 211241c50ccf garnett_macros.xml
--- a/garnett_macros.xml	Wed Apr 08 06:18:13 2020 -0400
+++ b/garnett_macros.xml	Fri Apr 24 11:21:40 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 2142ecf6ff02 -r 211241c50ccf garnett_transform_markers.xml
--- a/garnett_transform_markers.xml	Wed Apr 08 06:18:13 2020 -0400
+++ b/garnett_transform_markers.xml	Fri Apr 24 11:21:40 2020 -0400
@@ -5,7 +5,20 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}' --pval-col '${pval_col}' --pval-threshold '${pval_threshold}' --groups-col '${groups_col}' --gene-names '${gene_names}' --garnett-marker-file '${garnett_marker_file}'
+        transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}'  --garnett-marker-file '${garnett_marker_file}'
+
+        #if $pval_col
+        --pval-col '${pval_col}'
+        #end if
+        #if $pval_threshold
+        --pval-threshold '${pval_threshold}'
+        #end if
+        #if $groups_col
+        --groups-col '${groups_col}'
+        #end if
+        #if $gene_names
+        --gene-names '${gene_names}'
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="input_marker_file" format="txt" label="Input marker file" help="Path to the SCXA-style marker gene file in .txt format" />