# HG changeset patch
# User ebi-gxa
# Date 1587741600 14400
# Node ID 9d5e6a4ec5b555874ee164c615349bc43dd8272a
# Parent  196cc72cebd173f709e15225651b126a769585c2
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

diff -r 196cc72cebd1 -r 9d5e6a4ec5b5 ct_get_empirical_dist.xml
--- a/ct_get_empirical_dist.xml	Wed Apr 08 11:34:54 2020 -0400
+++ b/ct_get_empirical_dist.xml	Fri Apr 24 11:20:00 2020 -0400
@@ -6,9 +6,20 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-         ln -s $'${ontology_graph}' cl-basic.obo;
+        ln -s $'${ontology_graph}' cl-basic.obo;
+
+        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --output-path "${output_list_path}" 
 
-        get_empirical_dist.R --input-ref-file "${input_ref_file}" --parallel "${parallel}" --exclusions "${exclusions}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}" --num-cores "${num_cores}" --ontology-graph cl-basic.obo --semantic-sim-metric "${sem_sim_metric}" --output-path "${output_list_path}" ]]></command>
+        #if $parallel
+        --parallel "${parallel}"
+        #end if
+        #if $exclusions
+        --exclusions "${exclusions}"
+        #end if
+        #if $exclusions
+        --semantic-sim-metric "${sem_sim_metric}"
+        #end if
+        ]]></command>
     <inputs>
         <param type="data" name="input_ref_file" label="Input reference file" format="tsv" help="Text file with reference cell labels" />
         <param type="data" name="exclusions" format="yml" label="Exclusions file" help="YML file with excluded/unlabelled terms" />
@@ -16,7 +27,6 @@
         <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
         <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
         <param type="integer" name="num_iter" value='5' label="Number of iterations" help="Number of simulations to generate empirical CDF" />
-        <param type="integer" name="num_cores" value='4' label="Number of cores" help="Number of cores to run the process" />
         <param type="data" name="ontology_graph" label="Ontology graph" format="obo" help="Ontology graph to run semantis similarity computations" />
         <param type="text" name="sem_sim_metric" label="Semantic similarity metric" value="edge_resnik" help="Type of semantic similarity metric used" />
     </inputs>
diff -r 196cc72cebd1 -r 9d5e6a4ec5b5 ct_macros.xml
--- a/ct_macros.xml	Wed Apr 08 11:34:54 2020 -0400
+++ b/ct_macros.xml	Fri Apr 24 11:20:00 2020 -0400
@@ -29,7 +29,8 @@
             url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
           }
         </citation>
+        <citation type="doi">10.1101/2020.04.08.032698</citation>
         <yield />
       </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>