diff scmap_get_std_output.xml @ 1:656c588b718c draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

--- 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>