# HG changeset patch
# User ebi-gxa
# Date 1594639498 14400
# Node ID 424f8251a20279bc264f25e39e1a299a35c0efb2
# Parent  d15f7509077bc3548ff5b7ce1427ca4721bed420
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"

diff -r d15f7509077b -r 424f8251a202 ct_get_tool_perf_table.xml
--- a/ct_get_tool_perf_table.xml	Wed Jun 17 12:31:30 2020 -0400
+++ b/ct_get_tool_perf_table.xml	Mon Jul 13 07:24:58 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>Get performance table for a list of outputs generated by various tools</description>
     <macros>
          <import>ct_macros.xml</import>
@@ -10,16 +10,20 @@
           cp '$input_file' input_dir/;
         #end for
 
-        ln -s $'${ontology_graph}' cl-basic.obo;
-       
-        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1}   --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}"
+        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1}    --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}"
 
         #if $exclusions
         --exclusions "${exclusions}"
         #end if
+        #if $ontology_graph
+        --ontology-graph "${ontology_graph}"
+        #end if
         #if $parallel
         --parallel "${parallel}"
         #end if
+        #if $tmpdir
+        --tmpdir "${tmpdir}"
+        #end if
         #if $include_sem_siml
         --include-sem-siml "${include_sem_siml}"
         #end if
@@ -35,8 +39,8 @@
         #if $label_col_pred
         --label-column-pred "${label_col_pred}" 
         #end if
-        #if $semantic_sim_metric
-        --semantic-sim-metric "${semantic_sim_metric}" 
+        #if $sem_siml_metric
+        --semantic-sim-metric "${sem_siml_metric}" 
         #end if
 
          ]]></command>
@@ -52,7 +56,7 @@
         <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" />
         <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" />
         <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
-        <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" />
+        <param type="text" name="label_col_pred" label="Predicted file label column" value="predicted_label" help="Name of label field in predictions file" />
         <expand macro="sem_siml_options" />
     </inputs>
     <outputs>