# HG changeset patch
# User ebi-gxa
# Date 1606484330 0
# Node ID 90d7f30478ee16d2810101abeee84b018cec8946
# Parent  424f8251a20279bc264f25e39e1a299a35c0efb2
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"

diff -r 424f8251a202 -r 90d7f30478ee ct_get_tool_perf_table.xml
--- a/ct_get_tool_perf_table.xml	Mon Jul 13 07:24:58 2020 -0400
+++ b/ct_get_tool_perf_table.xml	Fri Nov 27 13:38:50 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Get performance table for a list of outputs generated by various tools</description>
     <macros>
          <import>ct_macros.xml</import>
@@ -10,7 +10,7 @@
           cp '$input_file' input_dir/;
         #end for
 
-        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 "${output_path}"
+        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" --tmpdir ./  
 
         #if $exclusions
         --exclusions "${exclusions}"
@@ -18,12 +18,6 @@
         #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
@@ -47,16 +41,22 @@
     <inputs>
         <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" />
         <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" />
-        <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
         <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
         <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" />
-        <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" />
-        <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
+        <param type="text" name="ontology_graph" label="Ontology graph" optional="true" help="Ontology graph to run semantis similarity computations" />
         <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
-        <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="predicted_label" help="Name of label field in predictions file" />
+        <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file">
+            <expand macro="sanitize_strings" />
+        </param>
+        <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file">
+            <expand macro="sanitize_strings" />
+        </param>
+        <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file">
+            <expand macro="sanitize_strings" />
+        </param>
+        <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="sanitize_strings" />
+        </param>
         <expand macro="sem_siml_options" />
     </inputs>
     <outputs>
@@ -66,13 +66,11 @@
         <test>
             <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" />
             <param name="ref_file" value="reference_sdrf.tsv" />
-            <param name="ontology_graph" value="cl-basic.obo" />
             <param name="lab_cl_mapping" value="label_cl_dict.rds" />
-            <param name="parallel" value="TRUE" />
             <param name="exclusions" value="exclusions.yml" />
             <param name="barcode_col_ref" value="Assay" />
             <param name="barcode_col_pred" value="cell_id" />
-            <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
+            <param name="label_col_ref" value="Sample Characteristic[cell type]"  />
             <param name="label_col_pred" value="predicted_label" />
             <output name="output_path" file="tool_perf_table.tsv" compare="sim_size" />
         </test>
diff -r 424f8251a202 -r 90d7f30478ee ct_macros.xml
--- a/ct_macros.xml	Mon Jul 13 07:24:58 2020 -0400
+++ b/ct_macros.xml	Fri Nov 27 13:38:50 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1.0</token>
+    <token name="@TOOL_VERSION@">1.1.1</token>
     <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.1.1">cell-types-analysis</requirement>
+        <requirement type="package" version="0.1.9">cell-types-analysis</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files
 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
 0.0.5+galaxy1: Standardise input/output format into .txt. 
     ]]></token>
@@ -34,6 +35,17 @@
             <option value="resnik">resnik</option>
         </param>
     </xml>
+    <xml name="sanitize_strings">
+        <sanitizer invalid_char="">
+        <valid initial="string.ascii_letters,string.digits">
+            <add value="_" />
+            <add value="-" />
+            <add value="[" />
+            <add value="]" />
+            <add value=" " />
+            </valid>
+    </sanitizer>
+    </xml>
     <xml name="citations">
       <citations>
         <citation type="bibtex">