# HG changeset patch
# User ebi-gxa
# Date 1587741951 14400
# Node ID 5593b0744de90983ddddacb62bbb02ab5d81546d
# Parent  dd2a84734b875b1adc23f9b36517ec5be901e0af
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r dd2a84734b87 -r 5593b0744de9 scmap_index_cell.xml
--- a/scmap_index_cell.xml	Fri Apr 03 06:36:06 2020 -0400
+++ b/scmap_index_cell.xml	Fri Apr 24 11:25:51 2020 -0400
@@ -5,12 +5,17 @@
     </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-cell.R --input-object-file "${input_single_cell_experiment}.preprocessed" --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+        scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
+        scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+        #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 name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" />
         <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" />
+        <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
         <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
     </inputs>
     <outputs>
diff -r dd2a84734b87 -r 5593b0744de9 scmap_macros.xml
--- a/scmap_macros.xml	Fri Apr 03 06:36:06 2020 -0400
+++ b/scmap_macros.xml	Fri Apr 24 11:25:51 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>