# HG changeset patch
# User ebi-gxa
# Date 1587741927 14400
# Node ID 9b60d5972dbda6c125f2a7e197725a2881fae9f8
# Parent  63f1a27dce34e06a4e62e9756665cc19137bfb35
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 63f1a27dce34 -r 9b60d5972dbd scmap_index_cluster.xml
--- a/scmap_index_cluster.xml	Fri Apr 03 06:35:36 2020 -0400
+++ b/scmap_index_cluster.xml	Fri Apr 24 11:25:27 2020 -0400
@@ -5,10 +5,14 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${input_single_cell_experiment}.preprocessed" && scmap-index-cluster.R --input-object-file "${input_single_cell_experiment}" --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
+        #if $train_id
+        --train-id '${train_id}' 
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
+        <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
         <param name="cluster_col" type="text" label="Cluster column" value="cell_type1" help="Column name in the 'colData' slot of the SingleCellExperiment object containing the cell classification information." />
     </inputs>
     <outputs>
diff -r 63f1a27dce34 -r 9b60d5972dbd scmap_macros.xml
--- a/scmap_macros.xml	Fri Apr 03 06:35:36 2020 -0400
+++ b/scmap_macros.xml	Fri Apr 24 11:25:27 2020 -0400
@@ -4,7 +4,7 @@
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.5">scmap-cli</requirement>
+        <requirement type="package" version="0.0.8">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -38,6 +38,7 @@
             url = {https://github.com/ebi-gene-expression-group/scmap-cli.git},
           }
         </citation>
+        <citation type="doi">10.1101/2020.04.08.032698</citation>
         <yield />
       </citations>
     </xml>