Mercurial > repos > ebi-gxa > garnett_transform_markers

diff garnett_transform_markers.xml @ 1:211241c50ccf draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:21:40 -0400
parents 2142ecf6ff02
children b35eef6b1fcc
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line diff
--- 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" />