# HG changeset patch
# User ebi-gxa
# Date 1587741853 14400
# Node ID 656c588b718c3d4ebbc8bf6071d5881dc7dafc2e
# Parent  5f95950c395956121873b20f32196a7554d8f130
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 5f95950c3959 -r 656c588b718c scmap_get_std_output.xml
--- a/scmap_get_std_output.xml	Fri Apr 03 06:33:57 2020 -0400
+++ b/scmap_get_std_output.xml	Fri Apr 24 11:24:13 2020 -0400
@@ -5,11 +5,16 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --sim-col-name "${sim_col_name}"
+        scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --index '${index}' --tool '${tool}' --sim-col-name "${sim_col_name}"
     ]]></command>
     <inputs>
         <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" />
         <param type="boolean" name="include_scores" checked="false"  label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" />
+        <param type="data" name="index" label="Scmap index object" format="rdata" help="Scmap index object in rdata format" />
+        <param type="select" name="tool" label="Tool used (cell/cluster)"  help="What tool was used - scmap-cell or scmap-cluster?">
+            <option value="scmap-cell">Scmap-cell</option>
+            <option value="scmap-cluster">Scmap-cluster</option>
+        </param>
         <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" />
     </inputs>
     <outputs>
diff -r 5f95950c3959 -r 656c588b718c scmap_macros.xml
--- a/scmap_macros.xml	Fri Apr 03 06:33:57 2020 -0400
+++ b/scmap_macros.xml	Fri Apr 24 11:24:13 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>